Manuals - Thermo Fisher Scientific

Manuals - Thermo Fisher Scientific
Affymetrix®GeneChip® Operating Software
With AutoLoader, Version 1.4
P/N 701439 Rev. 5
For research use only.
Not for use in diagnostic procedures.
Trademarks
®
, GeneChip®, HuSNP®, GenFlex®, Flying Objective™,
Affymetrix®,
CustomExpress®, CustomSeq™, NetAffx™, Tools To Take You As Far As Your Vision®,
and The Way Ahead™ are trademarks of Affymetrix, Inc.
GeneArray® is a registered trademark of Agilent Technologies.
All other trademarks are the property of their respective owners.
Limited License Notice
Limited License. Subject to the Affymetrix terms and conditions that govern your use
of Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable,
non-sublicensable license to use this Affymetrix product only in accordance with the
manual and written instructions provided by Affymetrix. You understand and agree
that except as expressly set forth in the Affymetrix terms and conditions, that no
right or license to any patent or other intellectual property owned or licensable by
Affymetrix is conveyed or implied by this Affymetrix product. In particular, no right or
license is conveyed or implied to use this Affymetrix product in combination with a
product not provided, licensed or specifically recommended by Affymetrix for such
use.
Patents
Scanner products may be covered by one or more of the following patents: U.S.
Patent Nos. 5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601;
6,141,096; 6,171,793; 6,185,030; 6,201,639; 6,207,960; 6,218,803; 6,225,625; 6,252,236;
6,335,824; 6,403,320; 6,407,858; 6,472,671; 6,490,533, and other U.S. or foreign
patents.
Software products may be covered by one or more of the following patents: U.S.
Patent No's. 5,733,729; 5,795,716; 5,974,164; 6,066,454; 6,090,555, 6,185,561
6,188,783, 6,223,127; 6,228,593; 6,229,911; 6,242,180; 6,308,170; 6,361,937; 6,420,108;
6,484,183; 6,505,125; 6510,391; 6,532,462; 6,546,340; 6,687,692; and other U.S. or
foreign patents.
Fluidics stations Products may be covered by U.S. Patent No. 6,114,122; and
6,391,623; 6,422,249; and other U.S. or foreign patents.
AutoLoader products may be covered by one or more of the following patents: U.S.
Patent Nos. 6,511,277; 6,604,902, and other U.S. or foreign patents.
Copyright
© 2003-2005 Affymetrix, Inc. All Rights Reserved.
iii
Table of Contents
CHAPTER 1
CHAPTER 2
CHAPTER 3
Welcome to the GeneChip® Operating System 3
INTRODUCING GENECHIP® OPERATING SOFTWARE
3
CONVENTIONS USED IN THIS GUIDE
3
RESOURCES
5
Installing GCOS
9
INSTALLING GCOS FOR NEW USERS
9
Affymetrix GeneChip® Library Install
INSTALLING LIBRARY FILES ON A NEW GCOS INSTALL
19
19
INSTALLING LIBRARY FILES ON AN UPGRADED GCOS INSTALL
CHAPTER 4
GeneChip® System Overview
25
37
SYSTEM OVERVIEW
37
GENECHIP® ASSAY
38
DATABASES
47
iv
CHAPTER 5
CHAPTER 6
CHAPTER 7
Affymetrix® GeneChip® Operating Software User’s Guide
Getting Started
53
STARTING GCOS
53
CHECKING THE GCOS DATA STORAGE SETTING
55
THE GCOS TRANSFER AND ANALYSIS SERVICES
56
GCOS USER INTERFACE
61
RENAMING A PROJECT, SAMPLE, OR EXPERIMENT
67
GCOS DATA
68
FILTERING DATA
71
CONFIGURING THE FLUIDICS STATION & SCANNER
73
Setting Up an Experiment
79
REGISTERING A SAMPLE & DEFINING AN EXPERIMENT
80
VIEWING OR EDITING AN EXPERIMENT
85
Sample History & Workflow Monitor
91
SAMPLE HISTORY
91
WORKFLOW MONITOR
95
Contents
CHAPTER 8
CHAPTER 9
Controlling the Instruments
v
105
THE FLUIDICS STATION
105
SCANNING A PROBE ARRAY–GENECHIP® SCANNER 3000
121
TRACKING CELL ANALYSES AND DATA TRANSFERS
133
Working with Images
141
INTRODUCTION
141
THE IMAGE WINDOW WITH CEL AND DAT FILES
145
VIEWING AND ALIGNING THE GRID AND SUBGRIDS
147
THE CELL SUMMARY REPORT
178
COMPUTING CELL INTENSITIES
195
ADJUSTING THE IMAGE SETTINGS
196
INTENSITY DISPLAY
204
CALCULATING AVERAGE INTENSITY FOR USER SPECIFIED
PROBE CELLS
205
VIEWING PROBE CELL DATA
206
VIEWING PROBE SET INFORMATION
207
BOOKMARKS
212
OUTLIERS
215
THE IMAGE VIEWER WITH JPG FILES
217
vi
CHAPTER 10
CHAPTER 11
Affymetrix® GeneChip® Operating Software User’s Guide
Gene Expression Analysis
225
OVERVIEW OF EXPRESSION ANALYSIS
226
EXPRESSION ANALYSIS SETTINGS
231
SINGLE-ARRAY EXPRESSION ANALYSIS
232
COMPARISON EXPRESSION ANALYSIS
235
EXPRESSION ANALYSIS TABULAR DATA
242
EXPRESSION ANALYSIS MEASURED IMAGES
256
EXPRESSION ANALYSIS GRAPHS
259
EXPRESSION REPORT
283
Batch Analysis
297
OPENING THE BATCH ANALYSIS WINDOW
298
SELECTING DATA FOR BATCH ANALYSIS
298
RENAMING RESULTS FROM BATCH ANALYSIS
306
REMOVING DATA FROM THE BATCH ANALYSIS WINDOW
308
RUNNING A BATCH ANALYSIS
309
EXPORTING A BATCH FILE
309
IMPORTING A BATCH FILE
310
Contents
CHAPTER 12
CHAPTER 13
CHAPTER 14
CHAPTER 15
Publishing Data
vii
315
SELECTING THE PUBLISH DATABASE
316
SPECIFYING THE TASK
316
PUBLISHING OPTIONS
320
PUBLISHING, CANCELING, OR RESTARTING A TASK
321
Defaults
327
VIEWING DEFAULT SETTINGS
327
FLUIDICS SETTINGS
333
SCANNER SETTINGS
334
ANALYSIS SETTINGS
335
Printing
341
PRINTING IMAGE OR CELL INTENSITY DATA
341
PRINTING PROBE ANALYSIS DATA
342
PRINTING AN EXPRESSION REPORT
343
GCOS Manager
347
GETTING STARTED
347
PROCESS TAB
356
viii
CHAPTER 16
Appendix A
Appendix B
Affymetrix® GeneChip® Operating Software User’s Guide
PUBLISH TAB
381
IMPORT TAB
396
USERSET TAB
415
TEMPLATE TAB
425
ROLES TAB
441
GCOS Administrator
455
GETTING STARTED
455
REGISTER OR UNREGISTER A GCOS SERVER
459
CHANGING A DATABASE PASSWORD
461
AUTOMATIC PROCESS DATABASE BACK UP
462
MANAGING WORKSTATION DATABASES
464
Client Testing
471
GCOS MANAGER 1.4 TESTING
471
GCOS 1.4 TESTING
493
DATA MINING TOOL 3.1 TESTING
518
GCOS MANAGER ADDITIONAL TESTING
523
Installing Data Mining Tool 3.1
DATA MINING TOOL 3.1
531
531
Contents
Appendix C
GCOS Instrument Installation
ix
541
THE AFFYMETRIX® SCANNER 3000 WITH FLUIDICS STATION
INSTALLATION
541
Appendix D
Appendix E
FLUIDICS STATION INSTALLATION (ONLY)
548
GENECHIP® SCANNER 3000 INSTALLATION (ONLY)
553
Using the GeneChip® Scanner 3000
561
INTRODUCTION
562
SAFE OPERATION
564
MAINTENANCE
568
CONNECTIONS AND INDICATOR LIGHTS
569
USING THE BARCODE READER
573
SCANNER 3000 SPECIFICATIONS
576
TROUBLESHOOTING
577
CE MARK DECLARATION OF CONFORMITY
583
REGULATORY
584
Configuring the GCOS Services
587
REQUIREMENTS FOR USING THE GCOS SERVICES
587
CONFIGURING THE GCOS SERVICE SETTINGS
589
SELECTING THE GCOS SERVICES OPTIONS
597
x
Appendix F
Appendix G
Appendix H
Affymetrix® GeneChip® Operating Software User’s Guide
SETTING THE START/STOP SERVICE POLICY
601
SETTING THE ACT AS PART OF THE OPERATING SYSTEM
POLICY
612
Expression Algorithm, Expression Analysis
Metrics & Settings627
EXPRESSION ANALYSIS ALGORITHM
627
EXPRESSION ANALYSIS METRICS
636
EXPRESSION ANALYSIS SETTINGS
644
CELL SUMMARY REPORT ALGORITHM
679
GCOS Data Types
685
PROBE INFORMATION (LIBRARY) DATA
685
FLUIDICS PROTOCOL DATA
685
EXPERIMENT DATA
686
Base Codes and Amino Acid Abbreviations 691
IUPAC BASE CODES
691
AMINO ACID ABBREVIATIONS
691
xi
Contents
Appendix I
Appendix J
Appendix K
Appendix L
Toolbars, Hot Keys, & Windowpanes
695
TOOLBARS
695
HOT KEYS
702
WORKING WITH WINDOWPANES & COLUMNS
705
RESIZING OR HIDING COLUMNS IN THE EAW
706
Database Management & Data Source Name
Descriptions709
PERFORMANCE TUNING FOR SQL SERVER
DATABASES
709
CLIENT TUNING
711
Troubleshooting
715
TROUBLESHOOTING QUESTIONS
715
GCOS 1.4 TROUBLESHOOTING
716
GCOS MANAGER 1.4 TROUBLESHOOTING
721
LIBRARY FILES TROUBLESHOOTING
727
Using the GeneChip® AutoLoader
731
SETTING UP THE AUTOLOADER
732
INSTALLING AND CONFIGURING THE E-MAIL SYSTEM
739
xii
Appendix M
Affymetrix® GeneChip® Operating Software User’s Guide
OPERATING THE SCANNER-AUTOLOADER
746
QUICK REFERENCE WALKTHROUGH
747
THE AUTOLOADER RUN
751
CLEANING AND MAINTENANCE
787
TROUBLESHOOTING
787
GENECHIP® SCANNER 3000 - AUTOLOADER SPECIFICATIONS
794
CE MARK DECLARATION OF CONFORMITY
795
REGULATORY
796
Data Transfer Tool Guide
801
USING THE DATA TRANSFER TOOL
801
ERROR MESSAGES AND TROUBLESHOOTING GUIDE
854
GCOS DATA COMPATIBILITY TABLE
865
Index
871
Chapter
1
Welcome to the GeneChip® Operating
System
Chapter
1
3
Welcome to the GeneChip® Operating
System
Welcome to the Affymetrix® GeneChip® Operating Software 1.4
User’s Guide. This manual explains how to use the following
applications:
• GeneChip® Operating Software (GCOS) 1.4 (formerly Affymetrix
Microarray Suite)
• GCOS Manager (formerly Affymetrix LIMS Manager)
• GCOS Administrator
Introducing GeneChip® Operating Software
GCOS 1.4 manages Affymetrix GeneChip array data. GCOS 1.4
manages data on the local work station using a Microsoft® Data
Engine database on the workstation. GCOS also has the ability to
connect with Affymetrix GeneChip Array Operating Software Server,
a separate application for large scale, network accessible databases.
GCOS, GCOS Manager, and GCOS Administrator are a trio of
applications that:
• Automate control of the GeneChip instruments.
• Capture and analyze the array image.
• Provide workflow tracking of experiment data (image, cell
intensities, probe analysis data).
• Manage experiment data.
• Automate basic expression analysis and publishing.
• Provide end user administration tools for workstation databases.
Conventions Used in This Guide
This manual provides a detailed outline for all tasks associated with
Affymetrix® GCOS, GCOS Manager, and GCOS Administrator.
Various conventions are used throughout the manual to help illustrate
the procedures described. Explanations of these conventions are
provided below.
4
Affymetrix® GeneChip® Operating Software User’s Guide
Steps
Instructions for procedures are written in a step format. Immediately
following the step number is the action to be performed. On the line
below the step there may be the following symbol: ⇒. This symbol
defines the system response or consequence that happens as a result of
user action; what you see and what has happened.
Following the response additional information pertaining to the step
may be found and is presented in paragraph format. For example:
1.
Click Yes to continue.
The Delete task proceeds.
In the lower right pane the status is displayed.
To view more information pertaining to the delete task, right-click
Delete and select View Task Log from the shortcut menu that
appears.
Font Styles
Bold fonts indicate names of commands, buttons, options or titles
within a dialog box. When asked to enter specific information, such
input appears in italics within the procedure being outlined.
For example:
Click the Find button
or select Edit → Find from the menu
bar.
The Find dialog box appears.
2. Enter AFFX-BioB-5_at in the Find what box, then click Find
Next to view the first search result.
3. Continue to click Find Next to view each successive search result.
1.
Screen Captures
The steps outlining procedures are frequently supplemented with
screen captures to further illustrate the instructions given. The screen
captures depicted in this manual may not exactly match the windows
displayed on your screen.
chapter 1 | Welcome to the GeneChip® Operating System
5
Additional Comments
Information presented in Tips provide helpful advice or shortcuts
for completing a task.
The Note format presents important information pertaining to the
text or procedure being outlined.
Caution notes advise you that the consequence(s) of an action may
be irreversible and/or result in lost data.
Warnings alert you to situations where physical harm to person or
damage to hardware is possible.
Resources
ONLINE DOCUMENTATION
The CD with GCOS includes an electronic version of this user’s guide.
The online documentation is in Adobe Acrobat® format (a *.pdf file)
and is readable with the Adobe® Acrobat Reader® software, available
at no charge from Adobe at http://www.adobe.com.
The online help contains a version of this user’s guide as a Microsoft®
HTML help file.
6
Affymetrix® GeneChip® Operating Software User’s Guide
TECHNICAL SUPPORT
Affymetrix provides technical support to all licensed users via phone
or E-mail. To contact Affymetrix® Technical Support:
Affymetrix, Inc.
3380 Central Expressway
Santa Clara, CA 95051 USA
E-mail: [email protected]
Tel: 1-888-362-2447 (1-888-DNA-CHIP)
Fax: 1-408-731-5441
Affymetrix UK Ltd.,
Voyager, Mercury Park,
Wycombe Lane, Wooburn Green,
High Wycombe HP10 0HH
United Kingdom
UK and Others Tel: +44 (0) 1628 552550
France Tel: 0800919505
Germany Tel: 01803001334
E-mail: [email protected]
Tel: +44 (0) 1628 552550
Fax: +44 (0) 1628 552585
Affymetrix Japan, K. K.
Mita NN Bldg
16 Floor, 4-1-23 Shiba,
Minato-ku, Tokyo 108-0014
Japan
Tel: +81 (03) 5730-8222
Fax: +81 (03) 5730-8201
www.affymetrix.com
Chapter
2
Installing GCOS
Chapter
2
9
Installing GCOS
This chapter provides detailed instructions for installing the
GeneChip® Operating Software (GCOS) for new users.
For information on installing the library files, see Chapter 3, Affymetrix
GeneChip® Library Install, on page 19. For information on installing the
instruments, see Appendix C, GCOS Instrument Installation, on page 541.
Installing GCOS for New Users
You must be logged in as an administrator to install GCOS.
The screen captures depicted in this manual may not exactly match
the windows displayed on your screen.
At least 1024 MB of available disk space is recommended for the
installation.
Insert the GCOS CD-ROM.
2. If the autorun feature does not start the program:
1.
Click Start → Run.
B. Type <cd drive letter>:\setup.exe.
C. Click OK.
The Affymetrix Software Setup window appears (Figure 2.1).
A.
10
Affymetrix® GeneChip® Operating Software User’s Guide
Figure 2.1
Install window
Click Install GCOS.
4. In the Welcome window (Figure 2.2), click Next.
The License Agreement windows appear (Figure 2.3).
3.
Figure 2.2
Welcome to GCOS setup
chapter 2 | Installing GCOS
Figure 2.3
License Agreement Window
5.
Review the contents and click Yes to accept the terms of the
licensing agreement.
The Customer Information window appears (Figure 2.4).
11
12
Affymetrix® GeneChip® Operating Software User’s Guide
Figure 2.4
Customer Information window
6.
Enter your Name, Company, and Serial Number.
The serial number is located on the Affymetrix® Software Product
Registration card.
If you do not have a serial number, contact Affymetrix Technical
Support.
7.
Click Next.
The GCOS Server Name window appears (Figure 2.5).
chapter 2 | Installing GCOS
Figure 2.5
GCOS Server Name window
Enter the name of the remote GCOS server that you want to
connect to. If you do not have one, leave the server name blank.
9. Click Next.
The Choose Destination Locations window opens (Figure 2.6).
8.
13
14
Affymetrix® GeneChip® Operating Software User’s Guide
Figure 2.6
Choose Destinations Locations window
10. Select
the destination where GCOS will be installed.
C:\GeneChip is the default location. If you are upgrading from
Microarray Suite, we recommend installing in the same directory.
11. Enter and confirm the password for the MSDE system
administrator (sa).
The password should be at least six characters long and must
contain at least two digits.
12. Click
Next.
The installation begins. When the install is completed, the GCOS
Software Setup Completed window appears (Figure 2.7).
chapter 2 | Installing GCOS
15
Figure 2.7
GeneChip Operating Software Setup Completed window
13. Choose
Yes, I want to restart my computer now, and click
Finish.
The system reboots.
If you are not prompted to reboot your computer, the installation
is complete.
If you are upgrading from a version of Microarray Suite, it is
necessary to run the library migrate program to migrate the library
files into the local database.
If GCOS will be used with a GCOS server, it is important to ensure
the library migration has been completed on the GCOS server.
16
Affymetrix® GeneChip® Operating Software User’s Guide
Chapter
3
Affymetrix GeneChip® Library Install
Chapter
3
19
Affymetrix GeneChip® Library Install
This chapter provides detailed instructions for installing Affymetrix®
GeneChip® probe array library files using the library install program.
The probe information or library data include the probe array design
characteristics, probe utilization and content, and scanning and
analysis parameters. Library data are unique to each probe array type.
The library install program includes a full install and an update
program. The full install should be used when installing the
Affymetrix GeneChip Operating Software (GCOS) on a new system. If
upgrading from a previous version of Affymetrix Microarray Suite, use
the library update program.
This chapter contains the following sections:
• Installing Library Files on a New GCOS Install (see below)
• Installing Library Files on an Upgraded GCOS Install (see page 25)
Installing Library Files on a New GCOS Install
This section of the manual guides you through the full library install
program. The full install is required on a GCOS system that was not
upgraded from a previous version of Affymetrix® Microarray Suite.
1.
Insert the library files CD-ROM for the appropriate probe array
type.
20
Affymetrix® GeneChip® Operating Software User’s Guide
The Affymetrix Library Files Setup window appears (Figure 3.1).
Figure 3.1
Library Files Setup window
2.
Click Full Library Install.
chapter 3 | Affymetrix GeneChip® Library Install
21
The InstallShield Wizard for Affymetrix Library Files starts
(Figure 3.2).
Figure 3.2
InstallShield Wizard Welcome window
GCOS does not allow you to modify the location of the library file
directory. By default, all probe array type information is installed in
the library subdirectory of the GCOS installation.
Do not move or delete the library directory or the files in the
directory. This will render the GCOS installation invalid.
3.
Click Next.
22
Affymetrix® GeneChip® Operating Software User’s Guide
The Select Probe Array Types window appears (Figure 3.3).
Figure 3.3
Select Probe Array Types window
Click Select All to select all array types for installation; or
Place a check mark next to the array type(s) that you want to
install.
For example, in Figure 3.3, the HG-U133A and HG-U133B
probe arrays will be installed on the system.
5. Click Next.
The Start Installing Files window appears (Figure 3.4).
This window shows the install options selected, including the:
- probe array types that will be installed on the system
- location of the library directory where the probe array library
data will be saved
- location of the protocol directory where the fluidic station
script files will be saved.
4.
chapter 3 | Affymetrix GeneChip® Library Install
Figure 3.4
Start Installing Files window
6.
Click Next.
The install process begins.
23
24
Affymetrix® GeneChip® Operating Software User’s Guide
After the installation is complete, the software displays the Finish
window (Figure 3.5).
Figure 3.5
Finish window
7.
Choose Yes, I want to view the Audit Report file now, and
click Finish.
The installation completes.
If an error occurs, the software displays an error dialog box
(Figure 3.6).
Figure 3.6
Error dialog box
chapter 3 | Affymetrix GeneChip® Library Install
8.
25
Click Yes to view the SQL.log and Audit XXX.log that contain
information about the error that occurred. Forward this file to
Affymetrix® technical support to obtain a solution for the
problem.
Installing Library Files on an Upgraded GCOS Install
The library install program includes a full install and an update
program. Use the update program when you upgrade from a version of
Affymetrix® Microarray Suite to GCOS. The update program migrates
probe array type information from the files in the library directory that
was used with Microarray Suite.
1.
Insert the library files CD_ROM for the appropriate probe array
type.
The Affymetrix Library Files Setup window appears (Figure 3.7).
Figure 3.7
Library Files Setup window
2.
Click Update Library Files.
26
Affymetrix® GeneChip® Operating Software User’s Guide
The InstallShield Wizard for Affymetrix Library Files starts
(Figure 3.8).
Figure 3.8
InstallShield Wizard Welcome window
3.
Click Next.
chapter 3 | Affymetrix GeneChip® Library Install
27
The Select Source Library Directory window appears (Figure 3.9).
Figure 3.9
Select Source Library Directory window
4.
To select the location of the source library directory from which to
migrate the information into the GCOS database, click Browse.
Click Next.
This library directory is the directory that was used with Affymetrix
Microarray suite. It contains .CIF and .CDF files that contain information
about the probe array types used in the system.
28
Affymetrix® GeneChip® Operating Software User’s Guide
The Select Source Protocol Directory window appears
(Figure 3.10).
Figure 3.10
Select Source Protocol Directory window
Click Browse and select the location of the fluidics protocols
directory from which to migrate the information into the GCOS
database.
6. Click Next to display the probe array types available for
migration.
5.
chapter 3 | Affymetrix GeneChip® Library Install
29
The Select Probe Array Types window appears (Figure 3.11).
To migrate a probe array type from a previous version of Microarray
Suite software, the library directory must contain the .CIF and .CDF
files. The update program will not install the gene descriptions,
sequences, or annotations. These should exist in the GCOS
database from the previous Microarray Suite install.
To migrate fluidics scripts from the protocols directory, the .BIN file
must exist along with the .MAC file. If the .BIN file is missing, the
software will not update the database with the associated script.
However, if a .BIN file exists in the directory without the associated
.MAC file (for example, the “Home” script that can be executed
without selecting an experiment) the update program will copy the
file to the new protocols directory.
Figure 3.11
Select Probe Array Types window
7.
Select the probe array types that you want to migrate from the
library directory. Click Select All to select all of the array types or
30
Affymetrix® GeneChip® Operating Software User’s Guide
place a check mark next to the probe array type(s) that you want to
install.
For example, in Figure 3.11, the RG-U34A probe array will be
installed on the system.
8. Click Next.
The Select Protocols window appears and displays the fluidics
protocols that will be migrated to the GCOS installation
(Figure 3.12).
Figure 3.12
Select Protocols window
Select the fluidics scripts that you want to migrate from the
protocols directory. To select all of the scripts, click Select All. To
select scripts individually, place a check mark next to the script.
For example, in Figure 3.12, the scripts EukGE-WS1v4, EukGEWS2v4, FlexGE-WS1v4, FlexGE-WS2v4 will be installed on the
system.
10. Click Next.
9.
chapter 3 | Affymetrix GeneChip® Library Install
31
The Start Importing Library Files window appears (Figure 3.13).
It shows the:
- probe array types and fluidics scripts that will be installed
- location of the library directory for the probe array type data
- location of the protocol directory for the fluidics station scripts
Figure 3.13
Start Importing Library Files window
11. Click
Next to start the installation.
32
Affymetrix® GeneChip® Operating Software User’s Guide
After the installation is complete, the software displays the Finish
window (Figure 3.14).
Figure 3.14
Finish window
12. Choose Yes, I want to view the Audit Report file now and click
Finish.
The installation completes.
If an error occurs, the software displays an error dialog box
(Figure 3.15).
Figure 3.15
Error dialog box
chapter 3 | Affymetrix GeneChip® Library Install
13. Click
33
Yes to view the sql.log and updateXXX.log files that
contain information about the error that occurred. Forward this file
to Affymetrix® technical support to obtain a solution for the
problem.
34
Affymetrix® GeneChip® Operating Software User’s Guide
Chapter
4
GeneChip® System Overview
Chapter
4
37
GeneChip® System Overview
This chapter provides background information on the Affymetrix®
GeneChip® array and instrument platform. It provides a brief
overview of the software applications that acquire, analyze, and
manage the data.
This chapter contains the following sections:
• System Overview (see below)
• GeneChip® Assay (see page 38)
• Databases (see page 47)
System Overview
The Affymetrix® GeneChip® platform uses high-density GeneChip
oligonucleotide probe arrays to efficiently acquire and analyze genetic
information. This integrated and complete system includes the:
• GeneChip® Hybridization Oven 640
• GeneChip® Fluidics Station
• GeneChip® Scanner 3000 scanner
• Computer workstation
• GeneChip® Operating Software (GCOS) 1.4 (formerly Microarray
Suite)
• GCOS Manager (formerly LIMS Manager)
• GCOS Administrator
• GeneChip® Operating Software Server (GCOS Server) (formerly
LIMS)
• Affymetrix® Data Mining Tool (DMT)
• GeneChip® Sequence Analysis Software (GSEQ)
• GeneChip® Genotyping Analysis Software (GTYPE)
38
Affymetrix® GeneChip® Operating Software User’s Guide
GeneChip® Assay
The GeneChip® Operating Software (GCOS) automates instrument
control and provides a central infrastructure to acquire, track, and
analyze experiment data. Table 4.1 shows the major steps and software
functions in a GeneChip® assay.
Table 4.1
GeneChip® Assay
Assay Step
Output
Software Function
Experiment
information
GCOS adds the sample and experiment
information to the process database. GCOS
tracks the sample and the associated
experiment data (image, cell intensities,
and probe analysis data) in the workflow
monitor.
Prepare the target.
Register the sample
and set up an
experiment.
Hybridize, wash, and
stain the probe array.
Scan the probe array.
GCOS automates control of the fluidics
station and scanner.
Image data
GCOS automates control of the scanner,
acquires and saves the scan data.
Cell intensity
data
GCOS automatically computes and saves
the cell intensities from the image data.
GCOS tracks the image and cell intensity
data in the process database.
chapter 4 | GeneChip® System Overview
39
Table 4.1
GeneChip® Assay
Assay Step
Output
Software Function
Analyze the cell
intensities.
Probe
analysis
The GCOS Statistical Expression algorithm
analyzes the cell intensities of expression
arrays, and saves the probe analysis or
chip data.
The GSEQ algorithms analyze the cell
intensities of resequencing GeneChip®
arrays, and saves the probe analysis or
chip data.
The GTYPE algorithms analyze the cell
intensities of other types of GeneChip®
genotyping and Universal Tag arrays, and
saves the probe analysis or chip data.
Generate a report.
Report (.rpt)
GCOS generates and saves the Expression
report (.rpt).
GSEQ and GTYPE generate and save a
report (.rpt) for array types other than
expression.
Publish the sample
and experiment data.
GCOS copies expression experiment data
(cell intensity and probe analysis data) to
the publish database where the data are
accessible to the Affymetrix® Data Mining
Tool (DMT) software and other third party
analysis tools.
GCOS provides a workflow-based tracking system for the data. The
workflow monitor (Figure 4.1) tracks sample or experiment status
through a series of steps or queue that includes:
• hybridization
• scan
• grid alignment
• cell intensity analysis (for image data files that require manual
grid alignment)
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Affymetrix® GeneChip® Operating Software User’s Guide
• probe array analysis for expression assay
• publish expression probe array analysis data
You can easily confirm the status of an experiment by checking the
workflow monitor. For example, the Hybridization tab shows
experiments to be processed in the fluidics station.
Figure 4.1
Workflow monitor, Hybridization tab
The workflow is further described in the following sections:
• Preparing the Target Sample, on page 41
• Registering a Sample and Setting Up an Experiment, on page 41
• Hybridizing, Washing, and Staining a Probe Array, on page 43
• Scanning a Probe Array, on page 43
• Computing Cell Intensities, on page 44
• Expression Analysis, on page 45
• Publishing Experiment Data, on page 46
chapter 4 | GeneChip® System Overview
41
PREPARING THE TARGET SAMPLE
Refer to the appropriate GeneChip® probe array package insert, the
Expression Analysis Technical Manual, or to other Affymetrix®
technical documentation relevant to your particular project.
REGISTERING A SAMPLE AND SETTING UP AN EXPERIMENT
You must identify or register a sample (target) and define an
experiment in GCOS before processing a probe array in the fluidics
station or scanning an array. You register the sample by entering the
sample type (required) and sample information (attributes), and
associating the sample with a project (which may include several
different samples) (Figure 4.2). The registration process adds the
sample information to the process database. Now GCOS tracks the
sample and the associated experiment data (image, cell intensities,
probe analysis data) in the workflow monitor.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 4.2
Sample and experiment information
To define an experiment, you specify the type of probe array to which
the target sample will be hybridized as well as other information
relevant to the experiment (Figure 4.2). You can also associate a
barcode with an experiment. If an Affymetrix® barcode is entered
(manually or using a keyboard wedge reader), GCOS automatically
reads and displays the probe array type, lot number, and expiration
date. GCOS uses the experiment information to select scanner
specifications for the probe array and identify the user-modifiable
algorithm parameters for data analysis.
You can also use a template (defined in GCOS Manager) to register a
sample and define an experiment. For more information on creating a
template, see Template Tab, on page 425.
chapter 4 | GeneChip® System Overview
43
HYBRIDIZING, WASHING, AND STAINING A PROBE ARRAY
During hybridization, the probe array is incubated with a
hybridization cocktail containing the labeled target and control
oligonucleotides in a buffer optimized for each type of probe array
(refer to the appropriate GeneChip® probe array package insert).
The hybridization reaction occurs in the GeneChip® fluidics station,
except for assays requiring longer hybridization periods in which case
the hybridization reaction occurs in the GeneChip® Hybridization
Oven 640.
During hybridization in the fluidics station, the probe array is
repeatedly filled and drained with the hybridization cocktail. The
strongest hybridization occurs between the array probes and sequences
in the target that are most nearly complementary.
After hybridization, the probe array undergoes a series of stringent
washes (specifically optimized for each type of probe array) in the
fluidics station. If the target was labeled with a fluorescent tag, the
array may be scanned at this point using the GeneChip® Scanner 3000.
In applications that use a biotin-labeled target, the probe array must
be stained with a streptavidin-conjugated fluorescent stain and
requires antibody amplification prior to scanning.
GCOS controls the fluidics station using pre-programmed fluidics
protocols for hybridizing, washing, and staining the probe arrays. The
computer workstation running GCOS can simultaneously control up
to eight fluidics stations. A fluidics station contains four modules and
each module can independently process a probe array using different
fluidics protocols. Some of the fluidics protocols may be customized.
Utilities for station maintenance are also included.
SCANNING A PROBE ARRAY
After the GeneChip® probe array has undergone hybridization,
washing, and staining, it is ready to be scanned.
GCOS automates control of the scanner and uses the experiment
information to manage the scanner settings for each type of probe
array. The software enables you to start a scan and view the intensity
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Affymetrix® GeneChip® Operating Software User’s Guide
data as it is collected during scanning. After the scan is completed,
GCOS displays a picture of the image data in the Image window
(Figure 4.3). GCOS tracks the image data and the scan parameters in
the process database. For more information on image data, see
Chapter 9, Working with Images, on page 141.
The Affymetrix® GeneChip® Scanner 3000 requires about 4 to 7
minutes to scan an array depending on the size of the scan region, the
number of scans, the autofocusing adjustment, and other parameters.
The Affymetrix® Scanner 3000 cannot scan fluorescein labeled
arrays.
COMPUTING CELL INTENSITIES
After the scan is completed, GCOS displays a picture of the scan image
in the image window. The software represents the fluorescence
intensity values from each pixel on the array in a grayscale or
pseudocolor mode and superimposes a grid on the image to delineate
the probe cells (features).
GCOS automatically:
• analyzes the image data and computes a single intensity value for
each probe cell on an array
• saves the cell intensity data (Figure 4.3)
GCOS tracks the cell intensity data and the parameters used in the cell
intensity analysis in the process database.
GCOS can be configured to archive the scan image locally or on a
network location. For more information, see Setting Archiving
Options for DAT files, on page 599.
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45
Figure 4.3
Image window, scan image (left) and computed cell intensity data (right)
EXPRESSION ANALYSIS
The Statistical Expression algorithm processes the cell intensity data.
A single-array analysis examines the cell intensity data from one
experiment (GeneChip® probe array). For each transcript represented
on the array, the algorithm computes the detection call (present,
absent, or marginal (unable to call the transcript present or absent), or
no call) and other call metrics.
A comparison analysis compares the cell intensities of the same probe
set on two different probe arrays (an experiment and baseline of the
same probe array type) to determine the relative change in the
expression level of a transcript. For each transcript represented on the
array, the algorithm computes the change call (increase, marginal
increase, no change, marginal decrease, decrease) or no call, and other
call metrics.
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Affymetrix® GeneChip® Operating Software User’s Guide
GCOS saves the probe analysis data and automatically displays it in
the Expression Analysis window (Figure 4.4). GCOS tracks the probe
analysis data and the analysis parameters in the process database.
Figure 4.4
Expression Analysis window, probe analysis data
GCOS analyzes expression cell intensity data only. GTYPE analyzes
cell intensity data from Mapping and Universal Tag probe arrays.
GSEQ analyzes cell intensity data from Resequencing probe arrays.
PUBLISHING EXPERIMENT DATA
GCOS copies or publishes expression experiment data (cell intensity
and probe analysis data) in AADM format to the publish database (see
Figure 4.5 on page 49). The publish database is accessible to the
Affymetrix® Data Mining Tool (DMT) or several other third party
chapter 4 | GeneChip® System Overview
47
analysis tools. The DMT is a separate application that provides
powerful query and analysis tools.
Databases
You can use GCOS installed as a stand-alone workstation or with a
networked GCOS Server.
If used as a stand-alone workstation, GCOS installs Microsoft® Data
Engine (MSDE) databases on the workstation. Table 4.2 shows the
GCOS databases and their functions.
Alternatively, the Affymetrix® GeneChip® Operating Software Server
(GCOS Server) installs Microsoft® SQL Server or Oracle® databases on
a network accessible server. GCOS also provides the end user interface
to GCOS Server. GCOS Server enables users to register samples and set
up experiments, and access and analyze data from any client
workstation on the network.
Table 4.2
GCOS databases
Database Name
Contents
Process
Data tracking information about samples and
experiments, and information about the image, intensity,
and probe analysis data for a particular sample and
experiment.
Publish
Expression data in the Affymetrix® Analysis Data Model
(AADM) database schema that can be accessed by the
Affymetrix® Data Mining Tool (DMT) and other software.
Gene Information
Accession numbers, probe set descriptions, target
sequence, and user annotations accessible to DMT.
DATABASE MANAGEMENT & ADMINISTRATION
GCOS Manager is a separate application that helps you manage your
expression data. This software tool provides a convenient way to:
• Manage the process and publish databases.
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Affymetrix® GeneChip® Operating Software User’s Guide
• Delete process or publish data.
• Create templates for entering sample and experiment attributes.
• Create a userset (a predefined set of Statistical Expression
algorithm parameter settings) for expression analysis.
• Archive image, cell intensity, and probe analysis data to a network
drive.
• Restore image, cell intensity, and probe analysis data to a network
drive.
• Export an experiment and the associated data files to a userspecified location on the workstation.
• Define user privileges (roles) for the GCOS server.
• Apply additional file security to the GCOS server.
For more information, see Chapter 15, GCOS Manager, on page 347.
GCOS Administrator enables you to:
• Monitor free and used workstation disk space.
• Change the location of a publish database.
• Change the password for the process database or a publish
database.
For more information, see Chapter 16, GCOS Administrator, on
page 455.
Together GCOS, GCOS Manager, and GCOS Administrator provide
full functionality for the GeneChip® instrument and array platform as
well as basic expression analysis (Figure 4.5).
chapter 4 | GeneChip® System Overview
Figure 4.5
GCOS, GCOS Manager, GCOS Administrator, and Data Mining Tool software
49
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Affymetrix® GeneChip® Operating Software User’s Guide
Chapter
5
Getting Started
Chapter
5
53
Getting Started
This chapter explains how to:
• Start the GeneChip® Operating Software (GCOS) (see below)
• Check the GCOS data storage setting (see page 54)
• Specify filters that determine the data displayed by the system
(see page 71)
• Configure the fluidics station and scanner (see page 73)
The chapter also introduces:
• The optional GCOS Services for automated data management
(see page 56)
• The GCOS interface (see page 61)
• GCOS data types (see page 68)
Starting GCOS
1.
Turn on the power for the computer workstation. If the
workstation is connected to the instruments, also turn on the
power for the GeneChip® Fluidics Station 400 and the
Affymetrix® GeneChip® Scanner 3000.
Laser in use during scanning.
The scanner laser should be turned on and warmed up at least 10
minutes before use. For more information, refer to Appendix D,
Using the GeneChip® Scanner 3000, on page 559.
2.
After the computer startup is complete, press Ctrl+Alt+Delete to
open the logon dialog box. Enter your user name, password, and
domain.
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Affymetrix® GeneChip® Operating Software User’s Guide
Click the Microsoft® Windows® Start menu button
, then
select Programs → Affymetrix → GeneChip Operating
Software.
When GCOS starts, the program displays the shortcut bar, data
tree, and status log (Figure 5.1).
The GCOS User interface is described in the following sections:
• Shortcut Bar (see below)
3.
• Data Tree (see page 64)
• Status Log (see page 67)
• Scan Status Window (see page 760)
After you have completed the above steps, you can configure the
GCOS software to:
• Run with a network accessible GeneChip Operating Software
(GCOS) server (see below).
• Use the optional GCOS Services for automated data management
(see page 56).
chapter 5 | Getting Started
55
Menu bar
Toolbar
Data Tree displays system data in the
process database that resides on the local
workstation or GCOS server. The data may
be filtered.
Main display area
Shortcut bar has three sections:
GeneChip Software
Instrument Control
Settings
Scan Status log
Status log
Figure 5.1
GCOS user interface (local database)
Checking the GCOS Data Storage Setting
The GCOS software may be configured to run with a network
accessible GeneChip® Operating Software (GCOS) Server or with an
MSDE database on the workstation.
To check the database setting to make sure GCOS is properly
configured for your system:
1.
In the Settings shortcut bar, click the Defaults button
Select Tools → Defaults from the menu bar.
The Defaults dialog box appears.
2.
Click the Database tab (Figure 5.2).
; or
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 5.2
Defaults dialog box, Database tab
The GCOS Server data storage option is available only if all
windows are closed and no instrument is active.
3.
To store experiment data on the GCOS server, choose the
Affymetrix GCOS option.
If the GCOS Server option is not selected, the data are stored in
the local MSDE database.
4.
Click OK.
The GCOS Transfer and Analysis Services
GCOS provides services that help you automate your data
management:
• GCOS Analysis Service performs cell intensity analyses.
If you are using GCOS with a networked GCOS Server, you can
chapter 5 | Getting Started
57
configure the software to run the analysis on the GCOS Server or
on the local instrument control client.
When analyzing data on the client (in local mode or in GCOS
Server mode), the software uses the service that runs on the local
workstation. When analyzing data on the GCOS Server (in server
mode), the software uses the analysis service on the remote GCOS
Server.
• GCOS Transfer Service lets you automate the archiving of DAT
files.
If you are performing a scan on a system configured to work with a
GCOS Server, and if GCOS is set up to analyze the DAT to CEL data
on the GCOS Server, you cannot use the transfer service to archive
data. This is the default mode.
You have several options for configuring the services, depending upon
the type of setup you have:
• Configuring the Analysis and Transfer Services on the Client (see
page 57)
• Configuring the Analysis Service on the GCOS Server (see page 60)
CONFIGURING THE ANALYSIS AND TRANSFER SERVICES ON THE CLIENT
The analysis/transfer service settings can be configured by opening the
service settings dialog from the Archive Settings tab or the Analysis
Settings tab on the GCOS Defaults dialog box (Figure 5.3).
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Affymetrix® GeneChip® Operating Software User’s Guide
Click
here
or
here
to open the GCOS Service
Settings dialog box
Figure 5.3
Defaults dialog box, Archive Settings and Analysis Settings tabs, and GCOS
Service Settings dialog box
The transfer service and analysis service use the same settings.
Changes made to one while using the service settings dialog will
automatically apply to the other service.
chapter 5 | Getting Started
59
There are two possible workstation configurations:
• Local analysis of DAT to CEL data on a workstation configured to work
without a GCOS Server
• Local analysis of DAT to CEL data on a workstation configured to work
with a GCOS Server
Local analysis of DAT to CEL data on a workstation
configured to work without a GCOS Server
The workstation configuration can be determined by looking at the
Database tab of the GCOS Defaults dialog. If the server name is
empty, the workstation was configured to work without a GCOS
server. For more information, see Checking the GCOS Data Storage
Setting, on page 55.
The services can run under the Windows SYSTEM account if
archiving is OFF (for information on setting the archive options see
Setting Archiving Options for DAT files, on page 599). If archiving is ON,
the service must be configured to run under the user credential who
has access to the Universal Naming Convention (UNC) path where
data is to be archived. Any changes to the analysis service user settings
are applied automatically to the transfer service settings.
For more information, see Configuring the GCOS Service Settings on a
Stand Alone System (No GCOS server), on page 591.
Local analysis of DAT to CEL data on a workstation
configured to work with a GCOS Server
The analysis /transfer service must be reconfigured to run as a user who
has admin rights on the local machine and is in the GCOS
Administrator's role on the GCOS Server. The list is populated
automatically with a list of users who have the above mentioned
rights.
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Affymetrix® GeneChip® Operating Software User’s Guide
For more information, see Configuring the GCOS Service Settings on a
Client Configured to Work with GCOS Server, on page 593.
CONFIGURING THE ANALYSIS SERVICE ON THE GCOS SERVER
The analysis service settings can be configured by opening the service
settings dialog from the control panel of Microsoft Windows
(Figure 5.4).
Open the Control Panel and
click the GeneChip Analysis
and Transfer icon
to open the GCOS Service
Settings dialog box for the
GCOS Server
Figure 5.4
Control Panel and GCOS Service Settings dialog box
The analysis service must be reconfigured to run as a user who has
admin rights on the local machine and is in the GCOS Administrator's
role on the GCOS Server. The list is populated automatically with a
list of users who have the above mentioned rights.
For more information, see Configuring the GCOS Service Settings on a
GCOS Server, on page 595.
chapter 5 | Getting Started
61
For more information on the following topics, refer to Appendix E,
Configuring the GCOS Services, on page 587:
• The requirements for using the Analysis and Transfer services (see
below)
• How to configure the GCOS Service settings (see page 589)
GCOS User Interface
The GCOS User interface is described in the following sections:
• Shortcut Bar (see below)
• Data Tree (see page 64)
• Status Log (see page 67)
• Scan Status Window (see page 760)
SHORTCUT BAR
The shortcut bar provides quick alternatives to menu bar commands.
The shortcut bar has three sections:
• GeneChip Software
• Instrument Control
• Settings
• To display a particular section of the shortcut bar, click the
shortcut bar section name (Figure 5.5 through Figure 5.6).
GeneChip® Software Shortcut Bar
Figure 5.1 shows the GeneChip Software shortcut bar at startup.
Additional buttons may be displayed in the shortcut bar, depending
on the data types that are open (Figure 5.5).
For example, if a scan image or cell intensity data are open, the
shortcut bar includes the Image Views button . Click this button
to view the cell intensity image in the main display area.
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Affymetrix® GeneChip® Operating Software User’s Guide
p
Shortcut Bar Functions
Click a button to change
the display of open data
in the main display area.
Set up an
experiment
or display
experiment
attributes
Display open
image or cell
intensities
Open the Batch
Analysis
window
Open the Publish
window
Open
the
sample
history
view
Open the
workflow
monitor
Display open
probe analysis
data in the
Expression
Analysis
window
Display an open report
(.rpt)
Figure 5.5
GeneChip® Software shortcut bar
chapter 5 | Getting Started
63
Instrument Control Shortcut Bar
Instrument Control
Shortcut Bar Functions
Click a button to perform
the following functions.
Open
Station
Selection
& Fluidics
Station
dialog box
Open the
Scanner
dialog
box
Figure 5.6
Instrument control shortcut bar
The instrument control shortcut bar does not display instrument
buttons if the workstation is not connected to the instruments, or if
the default configuration settings specify no fluidics station or
scanner installed (select Tools → Defaults from the menu bar to
view the default settings).
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Affymetrix® GeneChip® Operating Software User’s Guide
Settings Shortcut Bar
Settings Shortcut
Bar Functions
Click a button to perform
the following functions.
Open the
Defaults
dialog box
Open the
Filters dialog
box
Open the
Expression
Analysis Settings
dialog box
Open the
Expression Report
dialog box
Figure 5.7
Settings shortcut bar
DATA TREE
The data tree displays the data in the system (process database),
including:
• experiments
• image data
• cell intensities
• analysis results
chapter 5 | Getting Started
65
There are two different views of the data tree (Figure 5.8):
• Classic View organizes the experiment by data type.
• Project/Sample view organizes the experiment data by sample,
and samples are organized by project.
Classic View
Project/Sample View
Project
Sample
Experiment
Experiment data
includes image,
cell intensity, and
probe analysis
data
Figure 5.8
Data tree, Classic View (left), Project/Sample View (right)
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Affymetrix® GeneChip® Operating Software User’s Guide
Data Tree Display Options
• To select the data tree view, right-click the data tree and choose
Classic View or Project/Sample View from the shortcut menu
that appears.
• To collapse or expand the list of data types in the tree, click the
minus [-] or plus [+] sign next to each data type icon.
• To hide (or display) the data tree, click the Data Tree button
Data Tree Shortcut Menu
• To view a shortcut menu of commands (specific to the data type),
right-click a data name in the tree (Figure 5.9).
Figure 5.9
Data tree shortcut menu for cell intensities
From the data tree you can:
• Open an experiment, an image, cell intensity data, or probe
analysis data.
• Update the data source tree to show new information in the
system.
• Display information about the data (attributes).
.
chapter 5 | Getting Started
67
• Rename an experiment, sample, or project.
• Analyze an image (generate the cell intensity data).
• Analyze the cell intensity data from an expression probe array
(generates the probe analysis data).
• Generate an expression report.
STATUS LOG
The status log displays system status messages (Figure 5.1).
To clear the messages, right-click the status log and select Clear
Messages in the shortcut menu that appears.
2. To mute the error message sound, right-click the status log and
remove the check mark from the Play Error Sound option.
3. Click the Status Log button
in the main toolbar to hide (or
display) the status log.
1.
Renaming a Project, Sample, or Experiment
In the data tree project/sample view, you can rename an project,
sample, or experiment. In the data tree classic view, you can rename an
experiment.
1.
Right-click the data tree, and select Project/Sample View from
the shortcut menu that appears (Figure 5.10).
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 5.10
Data tree, project/sample view
2.
Expand the data tree, and right-click the item (project,
experiment, or sample) that you want to rename.
3.
Select Rename Project (Rename Experiment or Rename
Sample) in the shortcut menu that appears.
A Rename dialog box appears (Figure 5.11).
Figure 5.11
Rename Project dialog box
4.
Enter a new name and click OK.
GCOS Data
There are three types of GCOS data:
• Probe information or library files are unique for each probe array
type and contain information about the probe array design
chapter 5 | Getting Started
69
characteristics, scanning parameters, and default analysis
parameters.
• Fluidics protocol files define the hybridization, wash, or stain
protocols run by the GeneChip® Fluidics Station.
• Experiment data include the sample and experiment created by
the user when an experiment is defined, as well as the other data
types GCOS generates during an analysis: image data, cell
intensity data, and probe analysis data.
For more information about the data types, see Appendix G, GCOS
Data Types, on page 685.
OPENING DATA AND VIEWING INFORMATION
You can view information (attributes) about experiments, images, cell
intensity data, and probe analysis data.
In the data tree, double-click the data name; or
Right-click the data name in the tree and select Open from the
shortcut menu that appears.
This displays the data in the main display area.
Many data types may be open at the same time, but you can view
only one at a time in the main display area (except for a cascade or
tile view of images or cell intensity data).
2. Click a GeneChip Software shortcut bar button (Figure 5.5) to
toggle the view between the different types of open data.
1.
To view information about the data, right-click the data name in
the data tree and select Information in the shortcut menu that
appears.
An Information dialog box appears (Figure 5.12 and Figure 5.13).
4. To copy experiment data information to the system clipboard,
click Copy.
3.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 5.12
Experiment information (left) and image information (right)
chapter 5 | Getting Started
71
Figure 5.13
Cell intensity data information (left) and probe analysis data information (right)
Filtering Data
You may apply filters to the experiment data. The filters determine
the data that GCOS displays in the data tree, the sample history view,
workflow monitor, and the instrument control dialog boxes.
Filters are applied on a per user basis (identified by the logon name).
The filters you specify do not affect the filters specified by other users.
1.
Select Tools → Filters from the menu bar.
The Filters dialog box appears (Figure 5.14).
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 5.14
Filters dialog box
Make selections from the drop-down lists to specify the filters.
3. If you want to view the experimental data for a specific time
period, choose the Date From or To options and click the dropdown arrows to select calendar dates.
4. Click OK when finished to close the Filters dialog box and apply
the filters.
The status bar indicates that filters are applied (Figure 5.15).
2.
chapter 5 | Getting Started
73
Figure 5.15
Status bar in the lower right indicates filters applied
Configuring the Fluidics Station & Scanner
Before you use the fluidics station, check the fluidics station
configuration and prime the fluidics station with appropriate buffer.
For information on how to prime the fluidics station, and set up and
run a fluidics protocol, see Chapter 8, Controlling the Instruments, on
page 105.
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Affymetrix® GeneChip® Operating Software User’s Guide
The configuration process is described in the following sections:
• Configuring the Fluidics Station (see below)
• Configuring the Scanner (see page 75)
CONFIGURING THE FLUIDICS STATION
Before running a fluidics protocol, check to make sure the fluidics
station(s) is properly configured.
1.
Select Tools → Defaults from the menu bar.
The Defaults dialog box appears (Figure 5.16).
Figure 5.16
Defaults dialog box, Fluidics tab
Click the Fluidics tab.
3. Confirm the number of fluidics stations installed is correct or enter
a new value.
4. If desired, check mark Notification Message when protocol is
complete to display a notification message when a fluidics
protocol is completed.
2.
chapter 5 | Getting Started
5.
75
Click OK to close the Defaults dialog box.
CONFIGURING THE SCANNER
1.
Select Tools → Defaults from the menu bar.
The Defaults dialog box appears (Figure 5.17).
Figure 5.17
Defaults dialog box, Scanner tab
Click the Scanner tab.
3. If the workstation is connected to the scanner, choose the Scanner
Installed option.
4. To automatically turn the scanner laser on at startup, choose the
Turn on Laser at startup option.
2.
If the AutoLoader is present and you would like to disable the
autorun feature and add cartridges one by one, choose the Enable
Manual Mode option.
6. If the AutoLoader is present and you would like to disable it and
use the GCOS software without the AutoLoader, choose Disable
AutoLoader option.
5.
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Affymetrix® GeneChip® Operating Software User’s Guide
Chapter
6
Setting Up an Experiment
Chapter
6
79
Setting Up an Experiment
This chapter explains how to set up an experiment. You must define
an experiment in GCOS before processing a probe array in the fluidics
station or scanning a probe array. GCOS relies on the experiment
information to direct the scanner and apply the correct cell and data
analysis algorithms.
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 6.1
Assay & analysis flow chart
This chapter contains the following sections:
• Registering a Sample & Defining an Experiment (see page 80)
• Viewing or Editing an Experiment (see page 85)
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Affymetrix® GeneChip® Operating Software User’s Guide
Registering a Sample & Defining an Experiment
You identify, or register, a sample by entering sample information
(attributes) and associating the sample with a project (which may
include several different samples) (Figure 6.3).
To define an experiment, specify the type of probe array to which the
target (sample) will be hybridized as well as other information relevant
to the experiment. You may define one or more experiments per
sample (for example, the different probe arrays of a multiple probe
array set hybridized to the same sample).
You can associate a barcode with an experiment. If you entered an
Affymetrix® barcode (manually or using a keyboard wedge reader)
GCOS automatically reads and displays the probe array type, lot
number, and the expiration date. GCOS uses the experiment
information to select scanner specifications for the probe array and
identify the user-modifiable algorithm parameters for data analysis.
You can also use a template (defined in GCOS Manager) to register a
sample and define an experiment. For more information on creating a
template, see Template Tab, on page 425.
GCOS automatically adds the sample and experiment information to
the process database. This enters the experiment in the workflow and
enables you to track its status in the workflow monitor. After you
define an experiment, the Hybridization tab of the workflow monitor
displays the experiment and associated sample (Figure 6.2). The
Hybridization tab displays experiments that have not yet been
processed in the fluidics station. For more information about the
workflow monitor, see Workflow Monitor, on page 95.
The software uses sample and experiment information to maintain
relationships among the experiment data (image, cell intensity data,
probe analysis data), manage the workflow queue, and identify the
user-modifiable algorithm parameters for data analysis.
GeneChip® Operating Software Server supports expression,
Resequencing, Mapping, and Universal data.
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81
Sample Umb 243 is registered and associated with the ESC
project.
Workflow monitor
Workflow monitor tabs. Hybridization tab shows the
ESC1 experiment is defined, but not yet processed
in the fluidics station.
Figure 6.2
Workflow monitor, hybridization tab
1.
In the GeneChip Software shortcut bar, click Experiment Info
, or select File → New Experiment from the menu bar.
The Experiment Information tab appears (Figure 6.3).
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Enter information
here to register
the sample
Enter information
here to define
the experiment
Figure 6.3
Experiment Information tab
In the Experiment Information tab, items in bold are required
entries.
Enter a new sample name (up to 64 alphanumeric characters) or
select an existing sample name from the drop-down list. This is
required by GCOS. If you enter a new sample name, the sample
type and project are also required.
Or, if you want to use a sample template, make a selection from the
Sample Template drop-down list and enter the sample
information. A template specifies the information fields available
in the Experiment Information tab. You can define a template in
GCOS Manager. For more information on creating templates, see
Template Tab, on page 425.
3. Enter a unique experiment name (up to 64 alphanumeric
characters). This is required by GCOS. Or, if you want to use an
2.
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83
experiment template, make a selection from the Experiment
Template drop-down list and enter the experiment information.
The experiment name also serves as the name for the subsequent
data types generated during the analysis. For a description of
GCOS data types see Appendix G, GCOS Data Types, on page 685.
Make a selection from the Probe Array Type drop-down list
(required by GCOS).
5. You may add a barcode (up to 64 characters). Enter a barcode value
in the dialog box, or use a barcode reader to read the barcode
directly from the probe array cartridge.
If you use a barcode reader to read an Affymetrix® barcode from the
probe array cartridge:
- GCOS automatically fills in the probe array type, probe array
lot and expiration date fields.
- The Probe Array Type drop-down list is disabled.
4.
GCOS has the ability to store barcodes. You can enter barcode
information in either of two places: in the Experiment tab
(Figure 6.3) or in the Fluidics dialog box (see Figure 8.4 on
page 110). When you enter a valid barcode (maximum of 64
characters), GCOS stores the barcode with the experiment.
6.
To automatically publish expression probe analysis data:
Make a selection from the User Set drop-down list.
A user set is defined in GCOS Manager. The userset specifies the
values for the user-modifiable expression algorithm parameters.
For more information about user sets, see Userset Tab, on page 415.
B. Make a selection from the Publish Database drop-down list.
For more information about publishing data see Chapter 12,
Publishing Data, on page 315.
A.
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You must specify both a user set and a publish database, otherwise
the probe analysis data will not be published. If you specify only a
user set, the analysis proceeds using the analysis settings in the
Expression Analysis Settings dialog box, but the data are not
published. To view the Expression Analysis Settings dialog box,
click Expression Settings
in the Settings shortcut bar.
C.
To include the cell intensity data in the publish database,
choose the Publish Intensities option.
Publishing cell intensity data uses large amounts of computer
memory. For example, publishing the probe analysis data for a high
density probe array requires approximately 2 MB of disk space
compared to 30 MB for both the probe analysis and cell intensity
data.
7.
Click the Save button .
This saves the experiment and displays it in the data tree.
If you specified a user set and publish database during experiment
setup, the software prompts you for the publish database password
before the experiment is saved.
After the probe array is processed in the fluidics station and scanned,
click the Instrument Info tab to view information about the fluidics
protocol and scanning parameters captured by GCOS (Figure 6.4).
The instrument information page is blank until the probe array has
been processed in the fluidics station.
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85
Figure 6.4
Instrument Info tab
Viewing or Editing an Experiment
1.
To display an experiment, double-click the experiment name in
the data tree; or
Right-click the experiment name and select Open from the
shortcut menu that appears.
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To edit an entry, highlight the entry and enter the new
information; or
Right-click to open a shortcut menu of edit commands
(Figure 6.5).
Figure 6.5
Experiment information and shortcut menu of edit commands
3.
To clear all fields, select Edit → Clear from the menu bar
(equivalent to closing the experiment without saving).
When connected to a GCOS server database, only users authorized
by the System Administrator may delete data from the system
using the GCOS Manager software. When operating using the local
MSDE database, there is no data security.
4.
When finished, click the Close button
in the upper right
corner of the window or select File → Close from the menu bar.
chapter 6 | Setting Up an Experiment
Before the experiment is closed, GCOS prompts you to save
changes.
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Chapter
7
Sample History & Workflow Monitor
Chapter
7
91
Sample History & Workflow Monitor
This chapter explains how to use the sample history feature and
workflow monitor to track samples and experiment data. It contains
the following sections:
• Sample History (see below)
• Workflow Monitor (see page 95)
Sample History
The sample history feature provides two different views of the samples
in the system:
• Data view shows the experiment data derived from a particular
sample.
• Process view shows all stages (sample registration, experiment
setup, hybridization, scan, grid alignment, cell intensity analysis,
probe array analysis, and publishing) that are completed or
pending for a sample.
The following sections describe the sample history feature:
• Displaying Sample History (see below)
• Displaying Sample History Process View (see page 93)
DISPLAYING SAMPLE HISTORY
1.
In the GeneChip Software shortcut bar, click Sample History .
The sample history data view appears (Figure 7.1).
The data view is the default. If the data view is not displayed, select
View → Data from the menu bar.
The sample tree displays all assay samples. The expression folder
contains all registered expression analysis samples.
If filters have been applied, not all registered samples may be
displayed. For more information about filters, see Filtering Data, on
page 71.
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Sample history, data view
Click an item to
display property
values
Data tree
Sample tree
Click a sample in
the tree to display
experiment data
derived from the
sample
Property list
Figure 7.1
Sample history, data view
2.
To display a tree of the experiment data derived from a sample,
click the sample name in the sample tree.
3.
To display a list of data properties and their values (bottom right
pane), click an item in the sample history tree.
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93
DISPLAYING SAMPLE HISTORY PROCESS VIEW
The process view shows all completed or pending stages for a
particular sample.
1.
In the GeneChip Software shortcut bar, click Sample History
The sample history view appears.
.
2.
To display the process view (Figure 7.2), select View → Processes
from the menu bar.
The expression folder in the sample tree contains registered
expression analysis samples.
If filters have been applied, not all registered samples may be
displayed. For more information about filters, see Filtering Data, on
page 71.
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Data tree
Sample tree
Sample history, process view
Click a sample
in the tree
to display
processes
(completed or
pending) for
the sample
Click an item to display
property values
Property list
Figure 7.2
Sample history, process view
To display the sample history tree, click a sample name in the
sample tree.
Gray bullets indicate completed processes and green bullets
indicate those that are pending.
4. Click the plus sign [+] to the left of a process name to expand the
information in the sample history tree (Figure 7.2). Use the scroll
bars to the right or below the process tree to view the expanded
information.
3.
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95
The tree displays the inputs and outputs for each process. For
example, cell intensity data is the input to the probe array analysis
process that generates probe analysis data.
5.
To display a list of data properties (bottom right pane), click one
of the following in the sample history tree (Figure 7.2):
- sample name
- experiment name
- a process input or output
Workflow Monitor
When you define an experiment, it automatically enters the workflow
and may be tracked through the sequential tabs in the workflow
monitor (see Table 7.1).
Table 7.1
Workflow monitor tabs
Workflow Monitor
Tab
Displays...
Hybridization
Experiments that have not been processed in the
fluidics station.
Scan
Experiments that have been processed in the fluidics
station, but have not been scanned.
Grid Alignment
Image data that require manual grid alignment.
Cell Intensity Analysis
Image data that have been manually aligned, but
have not been analyzed by the cell analysis
algorithm (no cell intensity data exists)
Probe Array Analysis
Cell intensity data that have not been analyzed by
the expression analysis algorithm.
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Table 7.1
Workflow monitor tabs
Workflow Monitor
Tab
Displays...
Publish
Expression probe array analysis data that have not
been published.
Note: The GeneChip® Genotyping Analysis Software
(GTYPE) handles mapping and Universal Tag probe
array data for publishing queue purposes. The
GeneChip® Sequence Analysis Software (GSEQ)
handles resequencing probe array data for
publishing queue purposes.
The following sections describe the workflow monitor:
• Opening the Workflow Monitor (see below)
• Workflow Monitor Tabs (see page 98)
OPENING THE WORKFLOW MONITOR
1.
In the GeneChip Software shortcut bar, click Workflow
Monitor .
The workflow monitor appears (Figure 7.3).
If filters have been applied, not all registered samples or
experimental data may be displayed. For more information about
filters, see Filtering Data, on page 71.
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97
Data
tree
Workflow monitor
Shortcut
bar
Workflow monitor tabs
Figure 7.3
Workflow monitor, details view
2.
To update the display, select View → Refresh from the menu bar.
This refreshes the workflow monitor so that it displays any new
items added to the system since it was last opened.
To view a list of experiments, click the List button . To view
sample and project information for each experiment, click the
Details button .
4. To view experiment or data information, right-click the item and
select Open Item from the shortcut menu that appears; or
Select View → Open Item from the menu bar.
3.
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WORKFLOW MONITOR TABS
Click a tab to view the items in that part of the workflow queue.
2. To update the workflow monitor, select View → Refresh from the
menu bar.
1.
Hybridization Tab
The Hybridization tab displays experiments that have not been
processed in the fluidics station. An experiment is automatically
moved to the Scan tab after it has been processed in the fluidics station.
If a probe array is not processed (hybridized, or washed and stained) in
the fluidics station, the experiment must be manually advanced to the
Scan tab. To manually advance an experiment to the Scan tab:
• Right-click the experiment and click Advance to Scan in the
shortcut menu that appears; or
Click the experiment and select View → Advance to Scan from
the menu bar.
Scan Tab
The Scan tab displays experiments that have been processed in the
fluidics station, but have not been scanned. After the scan and grid
alignment processes are completed, the cell intensity analysis is
automatically run and the experiment is moved to the Probe Array
Analysis tab. If the grid was not successfully aligned by the Alignment
algorithm, the Grid Alignment tab displays the experiment.
Grid Alignment Tab
The Grid Alignment tab displays image data that require manual grid
alignment.
To manually align the grid:
1.
Right-click the image data in the Grid Alignment tab and click
Open Item in the shortcut menu that appears.
The image is displayed.
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2.
99
Align the grid at each corner of the image:
Click the
button in the Image window task bar and choose
a corner.
B. Place the mouse arrow over the grid (or sub-grid) perimeter (the
arrow becomes a double arrow,
).
The diagonal orientation of the double arrow along the
perimeter of a corner probe cell indicates horizontal and vertical
adjustments can be made simultaneously using the click-anddrag method or by using the keyboard arrow keys.
A.
Use the click-and-drag method or the keyboard arrow keys to
adjust the horizontal or vertical position of the grid so that it is
aligned over the corner of the image (Figure 7.4).
3. After you align the grid at each corner of the image, click the Save
button
(Figure 7.4).
The grid is saved.
C.
Figure 7.4
Manual grid alignment: align the grid at each corner of the image and click the Save button
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Cell Intensity Analysis Tab
The Cell Analysis tab displays image data after the grid has been
manually aligned. GCOS does not automatically generate the cell
intensity data from an image that requires manual grid
alignment. As a result, no cell intensity data exist for the image data
under the Cell Analysis tab.
To generate the cell intensity data:
• In the Cell Analysis tab, right-click the image and click Analyze
Item in the shortcut menu that appears.
This generates the cell intensity data and places it under the Probe
Array Analysis tab.
To generate the cell intensity data and probe array analysis data:
In the Cell Analysis tab, right-click the image and click Open
Item in the shortcut menu that appears.
This displays the image data.
2. Select Run Analysis from the menu bar.
This generates the cell intensity and probe analysis data.
The Publish tab displays the probe analysis data.
1.
Probe Array Analysis Tab
The Probe Array Analysis tab displays cell intensity data that have not
been analyzed by the expression analysis algorithm (no probe array
analysis data exists).
To analyze cell intensity data:
• In the Probe Array Analysis tab, right-click the cell intensity data
and click Analyze Item in the shortcut menu that appears; or
Select View → Analyze Item from the menu bar.
After the cell intensity data have been analyzed and the probe analysis
data have been generated, the experiment is moved to the Publish tab.
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101
Publish Tab
The Publish tab displays expression probe analysis data that have not
been published. The probe analysis data is removed from the Publish
tab and the workflow monitor after it is published.
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Chapter
8
Controlling the Instruments
Chapter
8
105
Controlling the Instruments
This chapter describes how to use the GeneChip® Operating Software
(GCOS) to control the GeneChip® Fluidics Station and the
Affymetrix® GeneChip® Scanner 3000 (Figure 8.1).
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 8.1
Assay & analysis flow chart
This chapter contains the following sections:
• The Fluidics Station (see below)
• Scanning a Probe Array–GeneChip® Scanner 3000 (see page 121)
• Tracking Cell Analyses and Data Transfers (see page 133)
The Fluidics Station
The fluidics station hybridizes, washes, and stains the probe arrays.
One workstation can control up to eight fluidics stations. Each fluidics
station contains four modules and each module can independently
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Affymetrix® GeneChip® Operating Software User’s Guide
process a probe array using a different fluidics protocol. Refer to the
GeneChip® Fluidics Station User’s Guide for a description of the
instrument, its components, and set up.
Before you use the fluidics station, check the fluidics station
configuration and prime the fluidics station with appropriate buffer.
For more information, see Configuring the Fluidics Station &
Scanner, on page 73.
The steps needed to use the fluidics station are described in the
following sections:
• Priming the Fluidics Station (see below)
• Setting Up a Fluidics Protocol (see page 109)
• Running the Fluidics Protocol (see page 110)
• Running a Maintenance Protocol in All Modules (see page 111)
• Resuming a Fluidics Protocol (see page 111)
• Bypassing Steps in a Fluidics Protocol (see page 112)
• Editing a Fluidics Protocol (see page 113)
• Editing the Fluidics ID Associated with a Fluidics Station (see
page 115)
PRIMING THE FLUIDICS STATION
Priming fills the fluidics station lines with wash buffers and deionized
water. The GeneChip® Fluidics Station must be primed before it can
be used to run assay protocols. Prime the fluidics station when:
• the fluidics station is first turned on
• a wash solution is changed
• the fluidics station is to be used again after a shutdown has been
performed
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107
• a module LCD window informs you that the module is not
primed
To prime the fluidics station:
Click the Fluidics button
in the Instrument Control shortcut
bar or the main toolbar; or
Select Run → Fluidics from the menu bar.
If more than one fluidics station is installed on the workstation, the
Station Selection dialog box appears (Figure 8.2).
If only one fluidics station is installed on the workstation, the
Fluidics Station dialog box appears (Figure 8.3).
2. If more than one fluidics station is installed on the workstation,
select the number designation of the current fluidics station from
the Station Number drop-down list.
1.
Figure 8.2
Station Selection dialog box
3.
Click OK to close the Station Selection dialog box.
The Fluidics Station dialog box for the currently selected station
appears (Figure 8.3).
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure 8.3
Fluidics Station dialog box, Prime protocol selected
4.
Select Prime from the Protocol drop-down list and No Probe Array
from the Experiment drop-down list for each module to be used.
Fill the intake buffer reservoirs A and B with the appropriate
priming buffer. (Refer to the appropriate GeneChip® probe array
package insert.)
6. Empty the waste bottle and fill the water reservoir with deionized
water.
5.
Load an empty, standard 1.5 mL microcentrifuge tube in the
sample holder of each module to be primed.
8. Click Run for each module to be primed and follow the prompts
in the fluidics station dialog box (also shown in the module LCD
window); or
To prime all modules, choose the All Modules option. Click Run
to start the priming on all modules and follow the prompts in the
Fluidics Station dialog box.
The Fluidics Station dialog box and the module LCD window
display the status of the procedure. The fluidics station is ready to
7.
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109
use when priming is completed and Priming done, Ready
appears in the module LCD window.
SETTING UP A FLUIDICS PROTOCOL
To set up the fluidics protocol:
1.
In the Instrument Control shortcut bar, click Fluidics ; or
Select Run → Fluidics from the menu bar.
If more than one fluidics station is installed on the workstation, the
Station Selection dialog box appears (Figure 8.2).
If only one fluidics station is installed on the workstation, the
Fluidics Station dialog box appears (Figure 8.4).
If more than one fluidics station is installed on the workstation,
select the number designation of the current fluidics station from
the Station Number drop-down list.
3. In the Fluidics Station dialog box (Figure 8.4):
2.
Select the current fluidics station module.
B. Choose an experiment and protocol from the drop-down lists.
(Refer to the appropriate GeneChip® probe array package
insert.)
C. If a barcode was entered when the experiment was created, enter
the barcode using the keyboard or scan the barcode with an
external barcode reader, and press the Tab key. This selects the
experiment associated with the barcode from the database.
4. If the selected experiment has no barcode, you can associate a
barcode with the experiment by entering the barcode using the
keyboard or an external barcode reader.
A.
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If filters have been applied, the Experiment drop-down list may not
include all experiments. Click Filter to open the Filters dialog box
and view or specify filters.
Choose the Include Hybridized Experiments option to include
hybridized experiments in the drop-down list.
Figure 8.4
Fluidics Station dialog box
Click View to display information about the selected experiment.
6. Click Run to start the protocol on the selected module.
7. Repeat as necessary for other modules in the fluidics station(s).
5.
RUNNING THE FLUIDICS PROTOCOL
To run the fluidics protocol:
1.
Load the probe array and sample vial holder containing the
appropriate solution in each active module.
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111
Sensors in the fluidics station detect when the probe array and
sample vial holder have been loaded. The process will proceed
automatically from this point, although some protocols may
require removal and substitution of the sample vial and solution.
The Fluidics Station dialog box and each module LCD window
display the status of the procedure.
2.
After the protocol is finished, remove the probe array and inspect
the probe array window for air bubbles.
If air bubbles are present, reinsert the probe array into the fluidics
station to automatically drain and refill the probe array with the
last wash buffer used. (Refer to the appropriate GeneChip® probe
array package insert.) If no bubbles are present, the probe array is
ready to be scanned.
RUNNING A MAINTENANCE PROTOCOL IN ALL MODULES
The software can start a maintenance protocol in all modules of the
fluidics station using a single button click. A maintenance protocol
(for example, CLEAN, DRAIN, HOME, PRIME, RECOVER,
SHUTDOWN, or BLEACH) does not require an experiment.
To run the maintenance protocol in all modules of the station:
Select a maintenance protocol from the Protocol drop-down list.
2. Select the All Modules option.
3. Click Run.
1.
RESUMING A FLUIDICS PROTOCOL
GCOS tracks the progress of a fluidics protocol run. If the protocol
stops before completion, it can be resumed at the point where it was
interrupted.
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The resume feature is only available for fluidics protocols that
display multiple steps in the Step drop-down list of the Fluidics
Station dialog box.
If you exit GCOS while a fluidics protocol is running, the resume
feature will be unavailable upon startup of GCOS.
To resume a fluidics protocol:
When ready to resume the protocol, select the appropriate protocol
from the Protocol drop-down list in the Fluidics Station dialog
box.
2. Select the All Modules option.
3. Click Run.
The selected protocol is started in modules one through four of the
fluidics station.
1.
BYPASSING STEPS IN A FLUIDICS PROTOCOL
Some multi-step fluidics protocols can be started at any step, so that
part of a protocol can be bypassed.
To bypass steps:
1.
In the Instrument Control shortcut bar, click Fluidics
Select Run → Fluidics from the menu bar.
The Fluidics Station dialog box appears (Figure 8.5).
; or
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113
Figure 8.5
Fluidics Station dialog box, bypassing protocol steps 1 and 2
2.
Select the desired experiment, module, and protocol from the
drop-down lists in the Fluidics Station dialog box.
The bypass function is only available for fluidics protocols that
display multiple steps in the Step drop-down list of the Fluidics
Station dialog box.
3.
Select the desired beginning step from the Step drop-down list
(Figure 8.5).
4.
Click Run to start the fluidics protocol at the selected step.
EDITING A FLUIDICS PROTOCOL
You can edit some hybridization and wash (Hybwash) protocols.
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Modifications to a Hybwash protocol must be completed before it
is run. Protocol changes made during a run do not affect the run in
progress.
To edit the protocol:
1.
Select Tools → Edit Protocol from the menu bar.
The Fluidics Protocol dialog box appears (Figure 8.6).
Figure 8.6
Fluidics Protocol dialog box
2.
Choose the fluidics protocol you want to edit from the Protocol
Name drop-down list.
Only the protocols in this list may be edited. All others are defined
for specific applications and cannot be customized.
3.
Highlight the parameter value you want to change and enter the
new value (Parameters values must be within the ranges in
Table 8.1). Enter a Hybridization Time of zero if only a wash is
chapter 8 | Controlling the Instruments
115
desired. To omit Wash A or B, enter zero for the Number of Wash
A or Wash B cycles.
Table 8.1
Valid ranges for hybridization or stain protocol parameters
Parameter
Valid Range
Hybridization or stain time
0 - 86,399 seconds
Temperature
15 - 50° C
Number of Wash cycles
0 - 99
Mixes per Wash cycle
1 - 99
To save the parameters under the same protocol name (overwrites
the old protocol), click Save.
5. To save the parameters under a new protocol name, enter a new
name in the Protocol Name field, then click Save.
This adds the new protocol name to the drop-down list.
6. Click Defaults to return the parameter settings to the default
values.
7. Click Delete to delete the currently selected protocol from the
system.
4.
EDITING THE FLUIDICS ID ASSOCIATED WITH A FLUIDICS STATION
GCOS has the ability to determine the fluidics station identity (ID)
and module number used to wash and stain a probe array. The local or
GCOS server database keeps track of the fluidics station ID and the
module number that processes an experiment (probe array).
To enable this feature, you must configure the registry using the
regedit application so that GCOS can read the fluidics station ID and
module number information from the registry.
To edit the fluidics ID:
1.
Click the Microsoft® Windows® Start menu button
select Run.
and
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The Run box appears (Figure 8.7).
Figure 8.7
Run box
2.
Enter regedit at the command prompt and click OK.
The Registry Editor appears (Figure 8.8).
Figure 8.8
Registry Editor
Open the HKEY_LOCAL_MACHINE registry hive.
4. Select the Software → Affymetrix → GeneChip → Fluidics
node under the HKEY_LOCAL_MACHINE registry hive
(Figure 8.9).
3.
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117
Figure 8.9
Registry Editor
5.
In the right window, right-click and select New → DWORD
Value from the shortcut menu to create a new name/data pair.
Repeat for each fluidics station whose ID is to be captured
(Figure 8.10).
GCOS allows a maximum of eight fluidics stations to be controlled
by a single workstation.
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Figure 8.10
Registry Editor. create new name/data pair
6.
Select the first newly created Name/Data pair, right-click the
name, and select Rename from the shortcut menu. Rename the
entry to “ID1”.
The example in Figure 8.11 shows four Name/Data pairs that have
been renamed ID1, ID2, ID3, and ID4.
chapter 8 | Controlling the Instruments
119
Figure 8.11
Registry Editor, four newly created Name/Data pairs renamed ID1, ID2, ID3, and
ID4
120
7.
Affymetrix® GeneChip® Operating Software User’s Guide
To edit the value of an entry, double-click the entry.
The Edit DWORD Value box appears (Figure 8.12).
Figure 8.12
Edit DWORD Value box
Select the Decimal option and enter a new value for the station ID.
9. Repeat step 7 and 8 to edit the value of each entry.
In this example, stations one through four have the ID 1001, 1002,
1003, and 1004 respectively (Figure 8.13). When a fluidics
protocol is run on any of these stations, the fluidics station ID and
the module number will be tracked in the process database.
8.
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121
Figure 8.13
Registry Editor
Scanning a Probe Array–GeneChip® Scanner 3000
This section shows you how to scan a GeneChip® probe array using the
Affymetrix® GeneChip® Scanner 3000. Before you scan a probe array,
make sure to read and understand:
• Appendix D, Using the GeneChip® Scanner 3000 (see page 561)
• Appendix L, Using the GeneChip® AutoLoader, on page 731
The steps needed to use the scanner are described in the following
sections:
• Using Tough-Spots® to Prevent Leaks (see below)
• Scanning a Probe Array (see page 124)
• Stopping a Scan (see page 132)
• Shutting Down the Scanner (see page 133)
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USING TOUGH-SPOTS® TO PREVENT LEAKS
Tough-Spots® are chemically inert polyvinyl labels that adhere to all
plastics. Affymetrix recommends using 3/8-inch circle diameter
Tough-Spots to prevent leakage from the cartridge septa.
Before loading the probe array cartridge, follow this procedure to
prevent the leaking of fluids from the cartridge during scanning.
Even if you have already applied Tough-Spots to the cartridge prior to
hybridization or after washing, you must remove the old Tough-Spots
and apply new ones before you load them into the AutoLoader.
Affymetrix recommends the use of Tough-Spots® obtained from
Affymetrix P/N 64-0158
or from
USA Scientific, Inc. P.O. Box 3565 Ocala, FL 34478 (800)LABTIPS P/N 9185-0000
To reduce the risk of leakage, do not use excessively large pipette
tips to pierce the septa.
To use Tough-Spots:
1.
On the back of the probe array cartridge, clean excess fluid from
around septa (Figure 8.14).
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Figure 8.14
The GeneChip® probe array cartridge
2.
Carefully apply one Tough-Spot over each of the two septa. Press
to ensure that the spots remain flat. If a Tough-Spot does not apply
smoothly; that is, if you observe bumps, bubbles, tears or curled
edges, do not attempt to smooth them out. Remove the spot and
apply a new one (Figure 8.15).
TM
Tough-Spots
Figure 8.15
Applying Tough-Spots® to cartridge septa
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SCANNING A PROBE ARRAY
To scan a probe array:
1.
Press the on/off (I/O) switch on the front panel. The scanner’s on
board computer will boot up. The bootup process takes a couple of
minutes. During this time both the yellow and green lights will be
on.
2.
Click the Start Scanner button
in the Instrument Control
shortcut bar or the main toolbar: or
Select Run → Start Scanner from the menu bar.
The Scanner dialog box appears (Figure 8.16). Note that the dialog
also displays barcode information if you entered it when you
created the experiment or set up the fluidics protocol.
Figure 8.16
Scanner dialog box, laser off (left) and laser on (right)
3.
To include scanned experiments in the Experiment Name dropdown list, choose the Include Scanned Experiments option.
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By default, the Experiment Name drop-down list displays the
experiments in the current directory that have not been scanned
(no image data exists for the experiments).
If filters have been applied, the drop-down list may not include all
experiments. Click Filter to open the Filters dialog box and view or
specify filters.
4.
Select the experiment name of the probe array to be scanned from
the Experiment Name drop-down list: or
Set the focus to the barcode field. If a barcode was associated with
the experiment to be scanned, scan or manually enter the barcode
from the probe array. This automatically retrieves the experiment
from the database.
The Probe Array Type field automatically displays the probe
array type that was entered during experiment setup. If a barcode
was entered when the experiment was created or hybridized, the
barcode field displays the barcode.
GCOS sets the Number of Scans per probe array type (generally
one for the Scanner 3000). You may change the number of scans in
the Scanner dialog box (Figure 8.16). Multiple scans are
statistically averaged to create the image data.
Increasing the number of scans increases the scan time as well as
the amount of fluorophore bleaching and may result in lower
fluorescence intensities.
5.
If it is necessary to rescan a probe array, select the experiment name
from the Experiment Name drop-down list. Also select Include
Scanned Experiments.
If you find it necessary to rescan a chip, GCOS appends an “_#” to
a new DAT file for the rescan operation
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Click Start in the Scanner dialog box.
When the software displays the Laser is On button in the scanner
dialog box, the Start button is activated and you can start a scan.
The GeneChip Scanner dialog box appears (Figure 8.17).
Figure 8.17
Scanner dialog box
The scanner door opens and the chip transport mechanism raises to
accept a probe array.
7.
Load the probe array (Figure 8.18) into the scanner chip transport
mechanism. Insert the probe array into the chip transport
mechanism such that the front of the probe array (label side) faces
to the rear of the scanner (Figure 8.19).
The scanner will enter Park mode if it is unattended for 15 minutes
and will enter standby, or sleep, mode if it is unattended for 60
minutes (45 minutes after entering Park mode). The green light will
turn off and the yellow light will turn on. To reactivate the laser,
click Turn Laser On in the scanner dialog box (Figure 8.16) and wait
10 minutes.
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Figure 8.18
Affymetrix® GeneChip® probe arrays: note the location of the flange. The
scanner will accept the probe array in only one orientation.
Do not force the probe array cartridge. If the cartridge does not drop
easily into the chip transport mechanism, eject the cartridge and try
again. If this does not remedy the situation, see Troubleshooting, on
page 577 or call Affymetrix technical support.
If a probe array becomes lodged in the scanner, you can manually
remove it. See Manually Removing a Lodged Probe Array Cartridge,
on page 579.
You cannot modify the scanner settings. GCOS automatically
selects the appropriate settings based on the probe array type
specified during experiment setup.
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Figure 8.19
Loading the probe array into the chip transport mechanism. Note that the front
of the probe array faces to the rear of the scanner.
8.
Click OK in the GeneChip Scanner dialog box to start scanning
the probe array.
During the scan, the green light will flash, and the yellow light
will be off.
After the scan starts, the software will start with the autofocus
routine. Data collection starts after successful completion of
autofocus. During the pre-scan state, when autofocus is complete,
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but before data collection has started, the software will count
downwards.
If the scan in progress feature is enabled (select View → Scan in
Progress from the menu bar), the Image window automatically
opens in the main display area when a scan starts. It displays the
fluorescence intensity of the probe array at approximately 50 lines
at a time as the scan progresses.
To enable (or disable) this option, select View from the menu bar
and place (or remove) a check mark next to Scan in Progress.
When multiple emission filters are used during the scan process,
the software will display the scan with a letter followed by the
percentage of scan completed. The letter identifies the scan
associated with the emission filter.
After the scan is completed, GCOS:
- Saves the image data (displayed in the main display area).
- Aligns a grid on the image to identify the probe cells.
- Saves the image data.
- Generates a JPG image from the DAT data.
- Ejects the probe array.
- Automatically closes the open image window.
- Submits the DAT file for archiving, if the archiving option has
been enabled in the Archive tab of the GCOS defaults dialog.
For more information, see Setting Archiving Options for DAT
files, on page 599.
If you are using GCOS on a workstation connected to a networked
GCOS Server, you can perform the CEL intensity analysis on the
workstation or on the GCOS Server.
When performing the analysis on the workstation, the DAT data is
submitted to the analysis service for computing CEL intensity
analysis. The DAT data and CEL data is transferred to the server after
completion of the CEL intensity analysis using the transfer service.
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When performing the analysis on the GCOS Server, the DAT and JPG
data is transferred immediately to the GCOS server. After the data is
copied, the software will submit the DAT data to the analysis service
for computing CEL intensity analysis.
For more information about configuring GCOS to work with a
networked GCOS Server, see The GCOS Transfer and Analysis
Services, on page 56.
If automation was used with this experiment, the transfer and
analysis services are not used for transferring the DAT data or for
generating the CEL intensity data
If you leave the scanner idle for an additional 15 minutes, the
scanner will also enter “Park” mode. The yellow light will be off and
the green light on.The chip transport mechanism will retract and
the scanner door will close. You must click the Eject Chip button to
open the scanner door and raise the chip transport mechanism.
SCANNING FOUR-COLOR ARRAYS
The four color scans are performed on GeneChip arrays that have been
configured for use with four emission filters. The four emission filters
are specified in the GCOS scan parameters. when performing a multifilter scan, GCOS scans the array with different emission filters, using
the order specified for the array.
A DAT file is created for each of the emission filter scans. To
distinguish the different scans, GCOS appends a suffix of A, B, C, or
D to the DAT files. Different file naming conventions are used in the
case of a rescan of an array, depending upon whether the array was
manually loaded (see below) or loaded using the autoloader
(see page 131).
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When running multiple scans on an array, the scanner performs
autofocus only once, prior to the first scan. This is true whether the
scans are performed as part of a four-color scan or as a re-scan.
Aborting a Scan with a Manually Loaded Array
If scanning is aborted on a manually loaded array, the emission filter
scan in progress continues until it is complete, and the DAT data for
the completed scans are saved. When the scan is resumed, GCOS
autofocuses the scanner and then re-scans and re-creates a DAT file for
each emission filter scan, overwriting the previously created DAT
files.
Aborting a Scan when Using the Autoloader
If scanning is aborted on an array loaded using the autoloader, the
emission filter scan in progress continues until it is complete, and the
DAT data for the completed emission scans are saved. When the scan
is resumed, GCOS autofocuses the scanner and then re-scans and recreates a DAT file for each emission filter scan. GCOS does not
overwrite the previously created DAT data, but creates a new set of
DAT files, adding a suffix of “_nX” to the DAT file name, where n
identifies the rescan number and 'X' is the letter assigned for the
emission filter. A 4-color array scanned a second time will produce
DAT files with the following suffixes: _2A, _2B, _2C, _2D.
When using the “Add Chips Now” function of the autoloader, if the
door is opened in the middle of a scan acquisition, GCOS treats the
scan as an abort request. After the emission filter scan in progress
completes, scanning halts and the DAT and CEL files for the
completed emission filter scans are saved. Upon resume, the GCOS
autofocuses the scanner and rescans the array for each emission
filter. To avoid the rescan of the array, it is recommended that the
“Add Chips Later” function be used.
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STOPPING A SCAN
Click the STOP button
or select Run → Stop Scanner from
the menu bar.
2. At the prompt, click Yes to stop the scanner or No to cancel
stopping (Figure 8.20).
1.
Figure 8.20
Stop scanner prompt
If you click Yes, the data from a partial scan will be lost. This is
different from using earlier software or scanner versions where you
could save the data from a partial scan.
If you rescan a probe array that has been partially scanned, the
previously scanned area of the probe array may experience
fluorophore bleaching. This will result in non-uniform fluorescence
intensity across the probe array.
3.
After you stop a scan, the scanner will automatically eject the chip.
The scanner dialog box (Figure 8.16 on page 124) has an eject chip
button. This is reserved for ejecting a chip after the scanner goes
into sleep mode or when you must manually eject the chip for any
other reason.
If the probe array cartridge becomes stuck, see Troubleshooting, on
page 577 or call Affymetrix technical support.
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SHUTTING DOWN THE SCANNER
Close the GCOS software.
2. Press the I/O (on/off) button on the front panel to turn off the
instrument.
1.
The laser also has a sleep mode that activates after 1 hour of
inactivity.
Tracking Cell Analyses and Data Transfers
The Analysis and Transfer Status window (Figure 8.21) allows you to
monitor the progress of cell intensity analyses and the archiving and
transferring of other DAT and CEL files.
For information about configuring the analysis and archive options see
Appendix E, Configuring the GCOS Services, on page 587.
To open the Analysis and Transfer Status window:
• Select Tools → Analysis and Transfer Status from the main
menu.
The Analysis and Transfer Status window opens (Figure 8.21).
Figure 8.21
Analysis and Transfer Status window
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The window displays the analyses and transfers as:
• Tasks: the analysis and transfer performed for each DAT file.
• Task items: the different steps used to complete each task (Figure
8.22).
Task
Task Items
Figure 8.22
Task and task items
The window has the following columns:
Task
Items being processed by the analysis and transfer services.
For more information, see Task Column, on page 134.
Status
The status of the analysis or transfer.
For more information, see Status Column, on page 135.
Description
Description of the task and reason for failure, if necessary.
For more information, see Description Column, on page 136.
The Restart Selected Task(s) button allows you to restart an
interrupted or failed task or task item (see Restarting an Interrupted
Task, on page 137).
ANALYSIS AND TRANSFER STATUS MESSAGES
Task Column
The Task column displays tasks and their associated task items.
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Task
For a task, the Task column displays the following information:
• <name of user who submitted task> - <start time>
Task Items
For a task item, the Task column displays the type of process:
• Analysis: the cell intensity analysis
• Transfer: transfer of DAT files to the archive location
Status Column
The Status column displays information about the progress of tasks
and task items.
Task
For tasks, the status column may display the following messages:
ACTIVE
The task is active.
WAIT
The task is waiting for processing.
ERROR
There was an error.
CANCELED
This task has been cancelled by the user
SUBMITING ITEMS
GCOS is in the process of submitting to the task, this task is
not available for processing.
Task Items
For task items, the status column may display the following messages:
ACTIVE
This item is active.
WAIT
This item is waiting.
ERROR
There was an error.
COMPLETE
This item is complete.
CANCELED
This item has been cancelled by the user.
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FILE WAIT
This item can not be processed because it is waiting for a
dependent file.
Description Column
The Description column includes information about the analyses and
transfers in progress, including the reasons for failure if necessary.
Analysis Descriptions
The description includes the following information for cell intensity
analyses:
• Analyze <number of files> files including <first file name>
• Analyze <file name>
When the cell intensity analysis is unsuccessful, the description also
includes a text description of the failure and its causes.
Transfer Descriptions
The description includes the following information for data transfers:
• Transfer <file name> to <path>
• Archive <file name> to <path>
When the transfer is unsuccessful, the description includes a text
description of the failure and its cause (Figure 8.23).
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Figure 8.23
Transfer error Message
RESTARTING AN INTERRUPTED TASK
An interrupted task can be restarted using the Analysis and Transfer
status controls.
To restart an interrupted task or task item:
Click on the task or task item to select it.
To select adjacent items, press and hold the Shift key while you
click the first and last item in the selection. To select non-adjacent
items, press and hold the Ctrl key while you click the items.
2. Click the Restart Selected Task button
; or
Right-click on the selected task or task item and select Restart
Selected Task(s) from the shortcut menu (Figure 8.24).
1.
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Figure 8.24
Shortcut menu
The task or task item is restarted.
Chapter
9
Working with Images
Chapter
9
141
Working with Images
The Image Window in GCOS 1.4 allows you to:
• View the Image data (.DAT)
• View a JPG file of the Image data
• Make adjustments to the gridding on the DAT file when
necessary
• View the Cell Intensity data (.CEL)
This chapter contains the following sections:
• Introduction (see below)
• The Image Window with CEL and DAT Files (see page 145)
• Viewing and Aligning the Grid and Subgrids (see page 147)
• The Cell Summary Report (see page 178)
• Computing Cell Intensities (see page 195)
• Adjusting the Image Settings (see page 196)
• Intensity Display (see page 204)
• Calculating Average Intensity for User Specified Probe Cells (see
page 205)
• Viewing Probe Cell Data (see page 206)
• Viewing Probe Set Information (see page 207)
• Bookmarks (see page 212)
• Outliers (see page 215)
• The Image Viewer with JPG Files (see page 217)
Introduction
You can open the Image Window by selecting the following file types
in the data tree or the Open Dialog box:
• .DAT files
• .JPG image of the DAT file
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• .CEL files
You can also set GCOS up so the Image Window automatically
displays the resulting DAT file during a probe array scan (for more
information, see Scanning a Probe Array–GeneChip® Scanner 3000, on
page 121).
Scroll bar
Image window
task bar
Scroll bar
Figure 9.1
Image data in the Image window
The Image window displays the data name (same as the experiment
name entered during experiment setup) in the upper left corner.
• Use the scroll bars at the bottom and right side of the Image
window to navigate the scan image.
You can learn more about using the Image window in the following
sections:
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• Opening Multiple Image Windows, on page 143
• Automatically Archiving Image Data, on page 144
• The Image Window with CEL and DAT Files, on page 145
• The Image Viewer with JPG Files, on page 217
OPENING MULTIPLE IMAGE WINDOWS
You can open and view more than one Image window in the main
display area.
After opening multiple files:
1.
Select Window → Cascade from the menu bar to display an
overlapping cascade of the open Image windows. Select Window
→ Tile to display the open Image windows side by side (Figure
9.2).
Figure 9.2
Multiple image windows, cascade view (left) and tile view (right)
2.
If other data types are open (for example, an experiment or probe
analysis data) and displayed in the main display area, click Image
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Views
in the GeneChip Software shortcut bar to display the
open Image windows.
AUTOMATICALLY ARCHIVING IMAGE DATA
DAT files may be stored locally or to a network location after the scan
is complete. A JPG file is always created, even if the image is not
archived.
The JPG file is a much smaller representation of the DAT file and is
meant to show large scale features in the image such as defects
(bubbles or scratches) and the general quality of the hybridization.
For more information about viewing JPG files, see The Image Viewer
with JPG Files, on page 217.
for more information about the archiving options, see Setting Archiving
Options for DAT files, on page 599.
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The Image Window with CEL and DAT Files
The Image window can be used to display DAT and CEL files
(Figure 9.3).
Image window
task bar
Figure 9.3
Image data in the Image window
You can learn more about using the Image window with DAT and
CEL files in the following sections:
• Commands in the Image Window Task Bar (see page 146)
• Viewing and Aligning the Grid and Subgrids (see page 147)
• Computing Cell Intensities (see page 195)
• Adjusting the Image Settings (see page 196)
• Intensity Display (see page 204)
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• Calculating Average Intensity for User Specified Probe Cells (see
page 205)
• Viewing Probe Set Information (see page 207)
• Bookmarks (see page 212)
• Outliers (see page 215)
COMMANDS IN THE IMAGE WINDOW TASK BAR
Figure 9.4
Task bar for CEL and DAT files
When viewing CEL and DAT files, the Image Window displays the
following controls in the task bar (Figure 9.4):
Auto
Automatically scales the intensity of the current image based on the range of
intensity levels in a selected region of the scan image. See Adjusting the Image
Settings, on page 196.
Adj.
Enables the subgrid adjustment.
Grid
Toggles the grid on and off the scan image. (Press the G key.) See Viewing the
Grid and Subgrids, on page 151.
Mask
Masks user selected areas of the scan image. Masked probe cells are
excluded from the analysis. See Outliers, on page 215.
Avg
Calculates the average intensity and standard deviation for a user selected
region of the scan image. See Calculating Average Intensity for User Specified
Probe Cells, on page 205.
In
Incrementally zooms in on the scan image. Press the I key: or
Use a click-and-drag operation to draw a rectangle over the area of interest,
then click In to zoom directly to the selected area.
Out
Zooms out incrementally from the scan image (press the O key).
Full
Zooms out completely to the full scan image view (press the Shift+O keys).
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Enables the user to select and zoom directly to each corner of the scan image
or selected subgrid to check grid alignment. See Viewing and Aligning the Grid
and Subgrids, on page 147.
SELECTING THE VIEW
To zoom in on an image:
• Click the In button in the task bar; or
Press the I key.
Holding the I key down performs a continuous zoom.
To zoom out on an image:
• Click the Out button in the task bar; or
Press the O key.
Holding the O key down performs a continuous zoom.
To zoom into a selected region:
Use the cursor to select the area of interest in the image.
A dashed box indicated the selected area.
2. Click the In button; or
Press the I key.
To zoom out completely:
• Click the Full button; or
Press the <Shift> + O keys
1.
Viewing and Aligning the Grid and Subgrids
The Alignment algorithm uses the checkerboard image of the control
probes, located at the corners of the probe array, to superimpose a grid
on the scan image. The algorithm aligns the grid so that each square
in the grid delineates a probe cell.
Some arrays use a single main grid (Figure 9.5).
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Figure 9.5
Array with a single grid
Other arrays use a main grid with multiple subgrids on the scan image
(Figure 9.6). The position of each sub-grid can be adjusted
independent of the other sub-grids.
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Figure 9.6
Main grid with subgrids
Each subgrid is identified by its row and column in the main grid. The
corners of each subgrid are marked on the chip by specific alignment
patterns; the anchors of the subgrid are aligned to these patterns
(Figure 9.7).
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corner
Figure 9.7
Corner patterns of a subgrid
The software uses the corner patterns at the 4 corners of the array to
come up with the initial main grid. The main grid is then divided into
smaller subgrids. The subgrid is aligned on the grid patterns in the
final steps of the gridding algorithm and in manual alignment. For
more information, see Aligning Subgrids, on page 162.
The alignment of the grid and subgrids usually takes place
automatically after scanning the chip. If the alignment algorithm fails
you can perform a manual alignment of the main grid and subgrids.
Learn more about working with grids and subgrids in:
• Viewing the Grid and Subgrids (see below)
• Aligning the Main Grid (see page 154)
• Aligning Subgrids (see page 162)
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VIEWING THE GRID AND SUBGRIDS
To toggle the grid on or off, do one of the following:
- Click Grid in the Image window task bar (Figure 9.1).
- Press the G key.
- Select View → Grid from the menu bar.
Figure 9.8
Main grid with subgrids
You can zoom in to view the grid or subgrids in more detail. When
viewing an array that uses a single grid, the individual cells are
displayed at higher magnifications (Figure 9.9).
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Figure 9.9
Zoom view of array with single grid, showing the individual cells
When viewing an array that uses subgrids, the Image window does not
display individual cells as a grid—instead, at smaller scales it displays
a small crosshair to mark the center of each cell of the grid
(Figure 9.10).
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Figure 9.10
Zoom view of chip with subgridding, feature centers indicated by crosshairs
You can change the color used to display the grid. For more
information, see Selecting Color Settings, on page 199.
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ALIGNING THE MAIN GRID
If the main grid is misaligned, you will see a notice after you scan a
probe array or try to open a DAT file (Figure 9.11).
Figure 9.11
Notice of main grid misalignment
You have two options for fixing an alignment problem:
• You can run the gridding algorithm again (see below).
• You can align the grid manually (see below)
Running the Gridding Algorithm
In some cases you can realign the grid by running the alignment
algorithm again.
To run the alignment algorithm again on an array that uses a single
grid:
• Right-click on the image and select Realign Grid from the
shortcut menu (Figure 9.12).
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Figure 9.12
Array with single grid and shortcut menu
To run the alignment algorithm again on an array that uses sub-grids:
• Right-click on the image and select Realign All Grids from the
shortcut menu (Figure 9.13).
This will align the main grid and all the subgrids.
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Figure 9.13
Array with subgrids and shortcut menu
After the alignment algorithm runs, click the Save button
select File → Save from the menu bar.
or
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Aligning the Grid Manually
If the grid alignment fails, an error message appears (Figure 9.14).
Figure 9.14
Notice of main grid misalignment
If you see the error message, you can manually adjust the main grid by
using the following procedure:
1.
Click the OK button in the error message.
The main grid is displayed in the Image window for an array with
a single grid (Figure 9.15) or an array using subgrids
(Figure 9.16).
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Figure 9.15
Misaligned main grid on an array with one grid
Subgrids will not be displayed if the main grid is misaligned.
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Figure 9.16
Misaligned main grid for probe array using subgrids
You can display the grid and subgrids for any DAT file by clicking
the Grid button in the Image window task bar.
2.
Align the grid at each corner of the image:
A.
Click the
a corner.
button in the Image window task bar and choose
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You may need to zoom out on the image to locate the grid
boundary.
Place the mouse arrow over the grid perimeter (the arrow
becomes a double arrow,
).
The diagonal orientation of the double arrow along the
perimeter of a corner probe cell indicates horizontal and vertical
adjustments can be made simultaneously using the click-anddrag method or by using the keyboard arrow keys.
C. Use the click-and-drag method or the keyboard arrow keys to
adjust the horizontal or vertical position of the grid so that it is
aligned over the corner of the outermost corner checkerboard.
For arrays that use a single grid, the software will display a box
around each feature when editing the grid (Figure 9.17).
B.
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Figure 9.17
Aligning on a chip with a single grid
When an array uses sub-grids and the main grid has failed to
align itself, then the software will display it with a single box
(Figure 9.18).
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corner
Figure 9.18
Aligning on an array with subgrids
Repeat the above steps for the other corners of the main grid.
3. After you align the grid, click the Save button
or select File →
Save from the menu bar.
The main grid is aligned.
For arrays with a single grid, you can now proceed to generate the
CEL file.
For arrays with subgrids, you can now check the alignment of the
subgrids.
Users have to select Realign Sub-grids to automatically create the
sub-grids using the main grid.
D.
ALIGNING SUBGRIDS
Sometimes one or more subgrids may require manual alignment. You
will be informed by the following notice when the subgrid alignment
fails (Figure 9.19):
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Figure 9.19
Notice of subgrid misalignment(s)
If the subgrid alignment fails you can:
• Run the subgrid alignment algorithm (see below).
• Perform a manual alignment (see below).
Running the Subgrid Alignment Algorithm
You can run the subgrid alignment algorithm if some of the subgrids
are misaligned or if you have manually aligned the main grid.
To run the subgrid alignment algorithm:
1.
Right-click the image and select Realign SubGrids from the
shortcut menu.
2.
After the alignment algorithm runs, click the Save button
select File → Save from the menu bar.
or
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Manually Aligning the Subgrids
The boundaries of a subgrid are indicated by the alignment patterns
at the four corners of the subgrid. A small checkerboard may mark the
corner of two or more subgrids, depending upon its position in the
main grid (Figure 9.20).
Figure 9.20
Subgrid borders
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If the sub-grids are not aligned correctly, the following error message
appears after scanning an array or opening a DAT file:
Figure 9.21
Notice of subgrid misalignment(s)
You can perform a manual alignment of the subgrids with the
following procedure:
1.
Click OK in the Subgrid Alignment Failure dialog box
(Figure 9.21).
The Manual Alignment alert opens (Figure 9.22).
Figure 9.22
Manual alignment alert
The subgrids are displayed in the Image window with the
misaligned subgrids highlighted by a red “X” (Figure 9.23).
You can display the grid and subgrids for any DAT file by clicking
the Grid button in the Image window task bar.
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Misaligned subgrids
Figure 9.23
Misaligned subgrids
You can change the color used to display the grid, the misaligned
subgrids, and the selected subgrid. For more information, see
Selecting Color Settings, on page 199.
2.
Click Yes in the manual alignment dialog box (Figure 9.22) to
perform a manual alignment.
The Manual Subgrid Alignment dialog box opens (Figure 9.24).
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Selected
subgrid
Defective
subgrids
Figure 9.24
the Manual Subgrid Alignment dialog box with misaligned and selected subgrids
You can also open the Manual Subgrid Alignment dialog box by
clicking the Adj. button in the Image window task bar.
The Manual Subgrid Alignment dialog box (Figure 9.25) allows
you to select a subgrid for adjustment and navigate to the corners
of the subgrid.
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Select the corner of the
subgrid to be aligned
Select the subgrid to be
aligned
Figure 9.25
Manual Subgrid Alignment dialog box
The dialog box has the following controls:
Subgrid List
Displays the subgrid and its position in the main grid by row
and column.
Go To Corner
buttons
Allows you to go to the subgrid corner you want to adjust.
Show All
Subgrids
Check to display all subgrids in the subgrid list (misaligned
subgrids are highlighted by a red X).
Subgrid
Displays the selected subgrid and its position in the grid
Corner
Displays the selected corner.
Close
Closes the dialog box.
You can use the + and - keys to step through the items in the
subgrid list.
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Click on the subgrid you wish to align in the list.
4. A zoomed-in view of the subgrid appears in the Image window.
3.
Figure 9.26
Selected subgrid
5.
Align the subgrid at each corner:
A.
Click the Go To Corner button for the corner you wish to
align.
A zoomed-in view of the corner of the subgrid appears
(Figure 9.27).
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When any one of the Go To Corner buttons is highlighted, the
software places a box around each feature to help with the grid
alignment. If the software is displaying the centers of features, as
explained on page 152, then the centers will not be displayed for
grids that have been manually aligned.
Figure 9.27
The upper right subgrid corner
B.
Place the mouse arrow over the grid perimeter (the arrow
becomes a double arrow,
).
The diagonal orientation of the double arrow along the
perimeter of a corner probe cell indicates horizontal and vertical
adjustments can be made simultaneously using the click-anddrag method or by using the keyboard arrow keys.
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C.
171
Use the click-and-drag method or the keyboard arrow keys to
adjust the horizontal or vertical position of the subgrid so that
it is aligned over the outside corner of the small checkerboard
pattern (Figure 9.28).
Figure 9.28
Dragging the subgrid boundary
Repeat steps a through c for the other corners.
E. Continue manually aligning all misaligned subgrids from the
subgrid list.
6. After you align the grid, click the Save button
or select File →
Save from the menu bar.
The grid is aligned.
You are now ready to recompute the cell intensities (see below).
D.
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TIPS FOR MANUALLY ALIGNING SUBGRIDS ON CUSTOMSEQ FOR
RESEQUENCING ARRAYS
Why would it be necessary to manually adjust grids on
subimages?
A subgrid may need to be manually gridded due to incorrect
corner placement, weak signals, debris, or other factors.
2. How would one know if there is a subgrid that needs to be
manually adjusted?
The Cell Summary Report in GCOS 1.4 provides a listing of
control probes which have unexpected intensities. These
unexpected intensities could be seeing bright intensities on
expected dim probes or vice versa. Examine the features on the
image that correspond to the control probes with unexpected
intensities. If they are not due to image debris then it is possible
they may be due to misgridding.
1.
3.
What do properly placed grids look like?
Properly placed grids are shown in Figure 9.29.
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Figure 9.29
Correctly placed grids
4.
What is the key item to look for when manually placing
grids?
The key item for placing grids vertically is the checkerboard
pattern (Figure 9.30).
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Figure 9.30
To position grids vertically
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The key item for placing the corner grids horizontally is the
sequence in the adjacent rows (Figure 9.31).
Figure 9.31
To position grids horizontally
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Please be careful when placing the subgrids manually because only
the checkerboard is available. The intensities of the extreme corner
cells are the only reference for manual alignment (Figure 9.32). In
fact, it is possible for the subgrid to look correct and be placed
incorrectly by two features.
Figure 9.32
Sub images only have the checkers for horizontal placement
5.
What do improperly placed grids look like?
Improperly placed grids are shown in Figure 9.33.
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Figure 9.33
Improperly placed grids
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The Cell Summary Report
The Cell Summary Report is a tool for monitoring the performance of
the hybridization and grid alignment of arrays. The report allows you
to detect problems in these steps and compare the performance of
different chips.
The Cell Summary Report uses the control features on the chip.
Control features are cells with special probes; the corresponding
targets are spiked into the sample cocktail. The resulting patterns of
bright and dark cells are used in grid alignment and other processes.
You can learn more about the Cell Summary reports in the following
sections:
• Generating a Cell Summary Report (see below)
• Cell Summary Report Components for Non-Resequencing Chips (see
page 181)
• Cell Summary Report Components for Resequencing Chips (see page 186)
• Cell Summary Report Settings (see page 189)
• Cell Summary Report Options (see page 190)
• Editing a Cell Summary Report (see page 192)
• Saving a Cell Summary Report (see page 193)
For more information about the algorithm used to generate the Cell
Summary report, see Cell Summary Report Algorithm, on page 679.
GENERATING A CELL SUMMARY REPORT
You must have a .GRC file for the chip type in the AffyData/Library
directory. The GRC files will be installed during the library
installation.
When working with a server, the GRC files need to be located in the
library folder on the server.
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To generate a cell-summary report:
1.
To generate the report, in the data tree, right-click the cell
intensity data for the report and select Report from the shortcut
menu that appears.
You can also select File → Report from the menu bar.
The Report dialog box opens (Figure 9.34).
Figure 9.34
Report dialog box
A.
From the Data of Type list, select CEL Data (*.CEL).
Select the Cell Intensity data for the report from the Data
Name list
C. Click OK.
This displays the Cell Summary Report in the main display area.
Figure 9.35 show an example Cell Summary Report.
B.
A previously generated report will be overwritten if the new report
is saved under the same name. To prevent overwriting old files,
save the report under a new name. For more information, see
Saving a Cell Summary Report, on page 193.
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You can also look at the failed cells in the Image window (see Outliers,
on page 215)
Report Header
Report
Summary
Metrics
List of failed
cells by subgrid
row and column
Figure 9.35
Expression Cell Summary report
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CELL SUMMARY REPORT COMPONENTS FOR NON-RESEQUENCING CHIPS
The Cell Summary Reports for all types of chips except Resequencing
(Expression, Mapping, and others) (Figure 9.35) provides information
on the following features:
• Non-synthesized features
• OligoB1 features
• OligoB2 features
Refer to the relevant manual for the GeneChip array for more
information about these features.
The report contains the following sections:
• Report Header (see below)
• Summary (see page 182)
• Metrics (see page 183)
• Failed Cell Locations (see page 184)
Report Header
Figure 9.36
Expression Cell Summary report: header
The report header (Figure 9.36) lists basic information about the Cell
Summary report:
Report Type
Used to distinguish types of reports (Cell Summary Report,
Algorithm Report, etc.).
Date
Time and date report was generated.
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Filename
Input .CEL data file name that was used to generate the
report.
GRC Filename
Name of the .GRC file used to generate the report.
Probe Array Type
Array type used for the .CEL file.
Summary
Figure 9.37
Expression Cell Summary report: Summary
The Summary (Figure 9.37) displays information:
For the following types of features:
Non-synthesized features
Bright control probes
Dim control probes
Total control features
The summary lists the following values:
Failures
The number of features in the category that failed.
Total
The total number of features in the category.
Failure Rate
The percentage of features in the category that failed.
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Metrics
Figure 9.38
Expression Cell Summary report: metrics
The metrics section (Figure 9.38) displays additional data about the
B1 and B2 oligos.
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Failed Cell Locations
Figure 9.39
Expression Cell summary report, failed cell locations
If the cell summary report was performed on a chip that used
subgridding, the report (Figure 9.39) displays the locations of the
failed features by row and column of the subgrid (Figure 9.40):
Row
Subgrid row.
Column
Subgrid column.
Total Failures
Total failures in the subgrid.
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To view these probes on a DAT file, the probes can be marked as
Masked. For more information about this option, see Cell Summary
Report Settings, on page 189.
Column
Row
1
2
3
4
1
2
3
4
5
6
7
8
9
10
11
12
13
Figure 9.40
Rows and columns in the subgrid
5
6
7
8
9
10
11
12
13
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CELL SUMMARY REPORT COMPONENTS FOR RESEQUENCING CHIPS
Resequencing chips do not have oligoB1 features. Instead, it provides
information on:
• Non-synthesized features.
• OligoB2 checker features (oligoB2 features arranged in a
checkerboard pattern).
• OligoB2 Extended features (oligoB2 features arranged in a
Resequencing pattern).
Refer to the relevant manual for the GeneChip array for more
information about these features.
The report (Figure 9.41) contains the following sections:
• Report Header (see below)
• Summary (see page 188)
• Metrics (see page 189)
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Report Header
Report
Summary
Metrics
Figure 9.41
Cell Summary report for resequencing chip
Report Header
Figure 9.42
Resequencing Cell Summary report: header
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The report header (Figure 9.42) lists basic information about the Cell
Summary report:
Report Type
Used to distinguish types of reports (Cell Summary Report,
Algorithm Report, etc.).
Date
Time and date report was generated.
Filename
Input .CEL data file name that was used to generate the
report.
GRC Filename
Name of the .GRC file used to generate the report.
Probe Array Type
Array type used for the .CEL file.
Summary
Figure 9.43
Resequencing Cell Summary report: Summary
The Summary (Figure 9.43) displays information:
For the following types of features:
Non-synthesized features
OligoB2 Checker
OligoB2 Extended control probes
Total control features
The summary lists the following values:
Failures
The number of features in the category that failed.
Total
The total number of features in the category.
Failure Rate
The percentage of features in the category that failed.
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Metrics
Figure 9.44
Resequencing Cell Summary report: metrics
The metrics section (Figure 9.44) displays additional information
about the non-synthesized and oligoB2 features.
USING THE CELL SUMMARY REPORT
The Cell Summary report provides clues to problems in the fluidics,
grid alignment, and other issues with the cell file.
It can be used to establish a baseline for performance, which can then
be used for quality control for subsequent experiments.
CELL SUMMARY REPORT SETTINGS
To change the masking of failed features:
1.
From the Menu bar, select Options -> Cell Summary Report.
The Cell Summary report dialog box opens (Figure 9.45).
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Figure 9.45
Cell Summary report dialog box
Click the Mask control Features checkbox.
3. Click OK.
The failed features will be displayed as masked features in the
Image window.
2.
CELL SUMMARY REPORT OPTIONS
You can perform the following operations on the Cell Summary
report:
• Changing Font and Tab Stops (see below)
• Searching the Report (see page 192)
• Editing a Cell Summary Report (see page 192)
• Performing a Search and Replace on the Report (see page 192)
• Saving a Cell Summary Report (see page 193)
Changing Font and Tab Stops
The Cell Summary report looks best when the default font and tab
settings of 10 point Arial font and 10 point tab stops are used.
To change the font:
1.
Select View → Set Font from the menu bar.
The Font dialog box opens (Figure 9.46).
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Figure 9.46
Font dialog box
Select the font, style, and size from the dialog box.
3. Click OK.
To change the tab stops and adjust the horizontal spacing of items on
a line:
2.
1.
Select View → Set Tab Stops from the menu bar.
The Set Tab Stops dialog box opens (Figure 9.47).
Figure 9.47
Set Tab Stops dialog box
Enter a tab value in the Tab Stop box.
3. Click OK.
2.
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Searching the Report
The Find feature searches the report.
1.
Click the Find button
or select Edit → Find from the menu
bar.
The Find dialog box appears (Figure 9.48).
Figure 9.48
Find dialog box
Enter the text for the search (up to 256 alphanumeric characters
including spaces) in the Find what box, then click Find Next to
view the first search result.
3. Click Find Next or the Find Next button
to view each
successive search result.
2.
Editing a Cell Summary Report
Edit commands for the cell summary report are available in the:
• Edit menu bar
• Report window toolbar
• Shortcut menu (right-click the report)
Performing a Search and Replace on the Report
The replace feature performs a text search and replaces the search item
with specified text.
1.
Select Edit → Replace from the menu bar.
The Replace dialog box appears (Figure 9.49).
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Figure 9.49
Replace dialog box
2.
Enter the text for the search in the Find what box and enter the
replacement text in the Replace with box.
3.
Click Find Next to begin the search, then click Replace to replace
the search item with the specified text. Repeat to find and replace
successive instances of the search item; or
Click Replace All to find and replace all occurrences of the search
item in the report.
Saving a Cell Summary Report
When GCOS generates a report for alignment probe analysis data, it
overwrites a previously generated report. To prevent a previous report
from being overwritten, save it under a new name.
1.
To open the report that you want to save under a new name, click
the Open button .
The Open dialog box appears (Figure 9.50).
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Figure 9.50
Open dialog box
Double-click the report name.
The report is displayed.
3. Select File → Save As from the menu bar.
The Save As dialog box appears (Figure 9.51).
2.
Figure 9.51
Save As dialog box
4.
Click the report to be saved, then enter a new name for the report
in the File name box.
5.
Click Save.
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Computing Cell Intensities
GCOS automatically generates the cell intensity data from the image
data (Figure 9.53). The Cell Analysis algorithm analyzes the image
data, computes a single intensity value for each probe cell on the array,
and saves the cell intensity data.
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 9.52
Assay & analysis flow chart
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Figure 9.53
Image window, scan image data (left) and computed cell intensity data (right)
REANALYZING IMAGE DATA
GCOS automatically generates the cell intensity data from the image
data. In some cases you may want to generate new cell intensity data
(for example, if the grid has been realigned).
To reanalyze image data:
• Right-click the open image and select Recalculate Cell Intensity
from the shortcut menu that appears.
Adjusting the Image Settings
You can adjust image settings (intensity range, color, coordinates, and
highlights) for image or cell intensity data. The image settings may be
adjusted for the current data only or globally for all subsequently
opened image or cell intensity data.
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MAKING ADJUSTMENTS TO THE CURRENT IMAGE OR CELL INTENSITY
DATA ONLY
To adjust the settings for the current image or intensity data only, do
one of the following:
• Click the Image settings button
.
• Press the S key.
• Select Edit → Image Settings from the menu bar.
This displays the Image Settings dialog box for the active image
or cell intensity data (Figure 9.54).
All settings (except the color setting) in the Image Settings dialog
box apply only to the current image or cell intensity data and do not
affect other image or intensity data. The settings (except for the
color setting) are not saved after you close the image or intensity
data.
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Click the S key
Select Tools → Defaults from
the menu bar
Settings for the active image or
cell intensity data only.
Default settings for subsequently
opened image or cell intensity data
Figure 9.54
Image Settings dialog box for the active image or cell intensity data (left);
Defaults dialog box, Image Settings tab (right)
MAKING GLOBAL ADJUSTMENTS TO SUBSEQUENTLY OPENED IMAGE OR
CELL INTENSITY DATA
To adjust settings globally:
• Select Tool → Defaults from the menu bar.
This displays the Image Settings tab of the Defaults dialog box
(Figure 9.54).
The settings specified in the Image Settings tab of the Defaults
dialog box do not affect open image or cell intensity data, but are
applied to all subsequently opened image or cell intensity data.
These default image settings are saved when the image is closed.
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SETTING THE INTENSITY RANGE
GCOS records a dynamic intensity range from 0 to 65,000 and
provides 256 colors from black through white for image display. The
intensity range for image or cell intensity data is divided into 256 bins
and each bin is assigned a color or gray scale.
You may enter a new lower or upper limit for the intensity range
associated with image or cell intensity data and apply this subset of the
dynamic range to the image. Lowering the upper limit increases the
image brightness and raising the lower limit decreases the brightness.
This process is called image scaling and can be used to adjust the display
of image or cell intensity data for optimum viewing. Alternatively,
GCOS can automatically scale the image using the minimum and
maximum pixel intensities of the image.
To autoscale the current image, choose the Autoscale option in
the Image Settings dialog box (Figure 9.54)
2. Click OK to automatically scale the image.
When the Image Settings dialog box is reopened, it displays the
minimum and maximum pixel intensities used to scale the image.
3. To return the intensity settings (autoscale option and intensity
range) to the defaults in the Defaults dialog box, click Defaults in
the Image Settings dialog box.
1.
SELECTING COLOR SETTINGS
To display the image or cell intensity data in:
• Gray scale - choose the Gray color option (Figure 9.54).
• Pseudo color - choose the Pseudo Color option.
This applies rainbow colors to the intensity scale.
To display a gray scale or pseudo color bar at the top of the Image
window:
• Choose the Color Bar option.
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SELECTING DISPLAY COORDINATES
• Click the image to display image coordinates.
A red cross hairs
marks the location.
The status bar (lower left in the main window) displays the
intensity data and x,y coordinates of a probe cell or pixel indicated
by the cross hairs.
If you choose the Cell option in the Image Settings dialog box
(Figure 9.54), the status bar and a pop-up tool tip display the x,y
coordinates of the cell, the cell intensity, and the pixel intensity
(Figure 9.55).
If you choose the Pixel option, the pop-up tool tip and the status bar
display the x,y coordinates of the pixel and the pixel intensity
(Figure 9.55).
Only the Cell option is available for cell intensity data.
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Cell X = 186, Y = 41, Cell Intensity = 22561.8, Pixel Intensity =
Figure 9.55
Image data, probe cell coordinates (top) and pixel coordinates (bottom)
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Pixel X = 1727, Y = 573, Intensity = 22409
Figure 9.55
Image data, probe cell coordinates (top) and pixel coordinates (bottom)
SPECIFYING HIGHLIGHT COLORS
You may specify new highlighting colors for the grid, masked cells,
outlier cells, or highlighted probe array cells (features).
1.
Click Highlights in the Image Settings dialog box (Figure 9.54 on
page 198).
The Highlight Colors dialog box appears (Figure 9.56).
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Figure 9.56
Highlight Colors dialog box
2.
To change the color of a particular item (for example, the grid
overlay):
Click the associated color box in the Highlight Colors dialog
box.
The Color palette is displayed (Figure 9.57).
A.
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Custom color
Luminosity
scale
Figure 9.57
Color palette
To select a predefined color, click one of the basic colors.
C. To define a custom color, click Define Custom Colors, then
use the click-and-drag method to move the cross hairs in the
custom color field. Adjust the color brightness using the
luminosity scale to the right. When finished, click Add to
Custom Colors to apply the color.
The new color is applied to the selected item.
D. Click OK to close the Color palette.
B.
Intensity Display
You can view the probe cell intensity in the image data as a measured
or difference image.
Open the image data.
2. Select View → Image from the menu bar, then choose one of the
two viewing options: Measured or Average.
1.
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MEASURED IMAGE VIEW
The measured image view (Figure 9.58) displays the raw data from a
scanned image.
Figure 9.58
Measured image view
AVERAGE IMAGE VIEW
The average image view (Figure 9.59) displays the probe cell intensity
values calculated by the Cell Analysis algorithm.
Figure 9.59
Average image view
Calculating Average Intensity for User Specified Probe
Cells
GCOS can calculate the average intensity for a user-specified group of
probe cells in the image data.
1.
In the image, use the click-and-drag method to select the probe
cells of interest.
The selected probe cells are outlined in the image.
2.
Click AVG in the Image window task bar (Figure 9.1 on
page 142).
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The status bar displays the average intensity and the standard
deviation.
3. Position the mouse arrow inside the selected area of the image.
A pop-up tool tip displays the average intensity and the standard
deviation for the selected group of probe cells (Figure 9.60).
Average Intensity = 17328, Std Dev =
Figure 9.60
Average intensity and standard deviation for user-specified probe cells in the
image data (.dat)
Viewing Probe Cell Data
You can click a probe cell (feature) in the image or cell intensity data
to obtain more information about the feature and the associated gene.
To display the probe cell data for image or cell intensity data, do one
of the following:
• Double-click the probe cell of interest.
• Click the probe cell of interest; right-click the image, and select
View Probe Cell Data in the shortcut menu that appears.
• Click a probe cell of interest and select View → Probe Cell Data
from the menu bar.
The Probe Cell Data dialog box appears (Figure 9.61).
Click other probe cells in the image to update the displayed data.
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Figure 9.61
Probe cell data, GeneChip® Hu6800 probe array
Cell Coordinates
The probe cell x and y coordinates in cell units.
Intensity
The cell intensity calculated by the cell analysis algorithm.
Probe Set
The identifier of the probe set containing the probe cell.
Direction
The direction (sense or antisense) of the target (sample).
Target Base
The expected nucleotide at the position that corresponds to the
substitution position of the probe.
Probe Base
The actual nucleotide located at the substitution position of the probe.
Position
The numbered position of the perfect match and mismatch probe pair
within the probe set (for example, 1-20 for a probe set consisting of
20 probe pairs).
Tile
The identification number for the probe set.
Viewing Probe Set Information
You can learn about viewing probe set information in:
• Viewing Probe Array Tiling Information (see below)
• Viewing Probe Cell Data for a Highlighted Probe Set(s) (see page 209)
• Highlighting Tiles on the Probe Array (see page 211)
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VIEWING PROBE ARRAY TILING INFORMATION
You can view probe array tiling information for the current image or
cell intensity data in the Image window.
1.
Right-click the image or cell intensity data and click View Probe
Tiling in the shortcut menu that appears: or
Select View → Probe Tiling from the menu bar.
The View Probe Tiling dialog box appears (Figure 9.62).
Figure 9.62
View Probe Tiling dialog box
The Features tab of the View Probe Tiling dialog box lists all probe
sets tiled on the probe array for the current image or cell intensity
data.
2.
In the Features tab, press and hold the Ctrl key while you click the
features of interest (Figure 9.62). Click Apply when the selection
is completed.
This highlights the probe sets in the image or cell intensity data
that correspond to the selected features so that hybridization data
may be quickly located (Figure 9.63).
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Figure 9.63
Highlighted probe cells in the image data
Turn off the grid (press the G key) so that the highlighted probe cells
can be easily seen. The highlighting color for the selected probe cells
may be changed. See Specifying Highlight Colors, on page 202.
3.
Click OK to close the View Probe Tiling dialog box.
VIEWING PROBE CELL DATA FOR A HIGHLIGHTED PROBE SET(S)
1.
In the image or cell intensity data, click a probe cell of interest.
This places the red cross hairs over the feature.
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Right-click and select View Probe Cell Data from the shortcut
menu that appears; or
Select View → Probe Cell Data from the menu bar.
This displays the probe cell data (Figure 9.64).
If you click another probe cell, GCOS automatically updates the
probe Cell Data dialog box.
Figure 9.64
Probe cell data for a selected feature
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To place the red cross hairs over the next feature of the highlighted
probe set, click the image (to return focus to the Image window)
and do one of the following:
- Press the N key.
- Right-click the image and select View Next Highlight in the
shortcut menu that appears.
- Select View → Next Highlight from the menu bar.
If it is open, the Probe Cell Data dialog box is automatically
updated with the new probe cell data.
4. To return the cross hairs to a previous feature, do one of the
following:
- Press the P key.
- Right-click the image and select View Previous Highlight in
the shortcut menu that appears.
- Select View → Previous Highlight from the menu bar.
3.
5.
To remove all highlights, do one of the following:
- Press the E key.
- Right-click the image and select Clear Highlights from the
shortcut menu that appears.
- Select View → Clear Highlights from the menu bar.
Highlights are automatically cleared when you close the image or
cell intensity data.
HIGHLIGHTING TILES ON THE PROBE ARRAY
You can highlight:
• all tiles or a particular tile on the probe array (by tile number)
• all positions or a particular position of all tiles or a selected tile
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Right-click the image or cell intensity data and click View Probe
Tiling in the shortcut menu that appears: or
Select View → Probe Tiling from the menu bar.
The View Probe Tiling dialog box appears (Figure 9.65).
2. Click the Positions tab, select a Position and Tile, then click
Apply.
This highlights the selection in the image.
Figure 9.65 shows two examples: all positions of tile number 3000
highlighted and only position 15 of tile 3000 highlighted.
1.
Figure 9.65
Cell intensity data, all positions of tile 3000 highlighted (left), position 15 of tile 3000 highlighted (right)
Bookmarks
A bookmark denotes a specific area of the image or cell intensity data
at a particular magnification level. Bookmarks make it easy to quickly
view the hybridization data at a specific location in different images.
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When you select a bookmark, the Image window automatically
displays the image location at the magnification specified by the
bookmark.
You can learn more about using bookmarks in:
• Creating a Bookmark (see below)
• Viewing Bookmarks (see page 214)
CREATING A BOOKMARK
Use the task bar zoom commands and scroll bars in the Image
window to locate the image area of interest at the desired
magnification level.
2. Right-click the image and select View Bookmarks → Add
Bookmark from the shortcut menu that appears; or
Select View → Bookmarks → Add Bookmark from the menu
bar.
The Add Bookmark dialog box appears (Figure 9.66).
1.
Figure 9.66
Add Bookmark dialog box
Enter a name in the Bookmark Name box or use the default name
Bookmark 1, 2,3....
4. Click OK to create the bookmark.
3.
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VIEWING BOOKMARKS
To view bookmarks, do either of the following:
• Right-click the image and select View Bookmarks → Edit
Bookmarks from the shortcut menu that appears; or
Select View → Bookmarks → Edit Bookmarks from the menu
bar.
The Edit Bookmarks dialog box displays a list of all the bookmarks
(Figure 9.67).
• Select View → Bookmarks from the menu bar. (A maximum of
20 bookmark names are displayed here.)
Figure 9.67
Edit Bookmarks dialog box
Commands in the Edit Bookmarks Dialog Box
Highlight the bookmark name in the Edit Bookmarks dialog box,
then click the command of interest.
Delete
Permanently removes the selected bookmark.
Rename
Allows the selected bookmark to be renamed.
Go To
Displays the selected bookmark in the image.
Close
Closes the Edit Bookmarks dialog box.
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Outliers
Outliers are probe cells that are obscured or non-uniform in intensity
(for example, probe cells with bright or dark streaks). The Outlier
Detection algorithm automatically determines whether a probe cell is
an outlier.
You can exclude or mask outliers from a probe array in an expression
analysis. The Statistical Expression algorithm (generates the probe
analysis data from the cell intensity data) ignores the probe cell data
from masked outliers.
Learn more about working with outliers in:
• Viewing Outliers (see below)
• Masking Outliers (see page 216)
• Unmasking Outliers (see page 217)
When an array uses sub-grids, outliers will not be displayed in the
image.
VIEWING OUTLIERS
1.
Open the image or cell intensity data of interest.
2.
Right-click in the Image window and select View → Cells
Masked from the shortcut menu; or
Select View → Cells → Outliers from the menu bar.
This highlights outlier probe cells with diagonal lines
(Figure 9.69).
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Figure 9.68
Highlighted cells
The color that highlights outliers may be changed. See Specifying
Highlight Colors, on page 202.
MASKING OUTLIERS
Open the image or cell intensity data of interest.
2. Select Edit → Mask All Outliers from the menu bar.
All outliers identified by the Outlier Detection algorithm are
masked.
3. To mask user-specified probe cells:
1.
Use the click-and-drag method to select a probe cell or area of
the image to be masked.
B. Select Edit → Mask Cells from the menu bar.
A.
Turn off the grid (press the G key) to easily view the masked probe
cells highlighted with diagonal lines.
4.
To view masked probe cells, right-click in the Image window and
select View Cells → Masked from the shortcut menu that
appears.
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UNMASKING OUTLIERS
Select Edit → Unmask All Cells from the menu bar.
This removes all masking.
2. To unmask only a selected probe cell or area:
1.
Use the click-and-drag method to select a probe cell or area of
interest.
B. Select Edit → Unmask Cells from the menu bar.
A.
If you manually adjust the grid or change the probe array type in the
experiment, the mask or outlier data will be lost when new cell
intensity data are generated.
The Image Viewer with JPG Files
DAT files may be stored locally or to a network location. A JPG
format file is created to allow the user to look at the image for basic
QC purposes.
The JPG file takes up much less memory than the DAT file and is
meant to show large scale features in the image such as defects
(bubbles or scratches) and the general quality of the hybridization.
You can display these JPG files in the Image window to evaluate
hybridization quality. The Image window functions are described in
the following sections:
• Opening a JPG Image (see below)
• The JPG View Task Bar (see page 219)
• Selecting the View (see page 220)
• Adjusting Brightness and Contrast (see page 221)
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OPENING A JPG IMAGE
To open a JPG image:
• Right-click on the DAT file and select Open JPG from the
shortcut menu that appears (Figure 9.69); or
Figure 9.69
Selecting the JPEG file in the data tree
• Select File → Open from the main menu.
The Open dialog box opens.
Select JPG Data (*.JPG) from the Data of Type list.
B. Select the JPG file you wish to open from the File Name list.
C. Click OK.
The JPG image is displayed in the JPG Viewer (Figure 9.70).
A.
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JPG Image window
task bar
Figure 9.70
JPG image in the Image window
THE JPG VIEW TASK BAR
When viewing JPG files, the Image window displays the following
controls in the task bar (Figure 9.70):
In
Zooms in incrementally on the image.
Out
Zooms out incrementally on the image.
Full
Zooms out to the full scan image.
Figure 9.71
JPG View task bar
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SELECTING THE VIEW
You can click the In and Out buttons to magnify the image, or the
Full button to return to the full scan image view.
To zoom in on a particular area:
1.
Select View → Zoom → Zoom to Selected Region from the
main menu; or
Right-click in the image and select Zoom to Selected Region
from the shortcut menu (Figure 9.72).
Figure 9.72
Shortcut menu in JPG view
2.
Use the cursor to select the area of interest in the image.
A dashed box indicated the selected area.
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When you release the mouse button, the selected area fills the
Image Viewer.
To zoom in without selecting an area:
• Select View → Zoom → Zoom In from the main menu; or
Click the In button in the Image window task bar.
To zoom out on an area:
• Select View → Zoom → Zoom Out from the main menu; or
Click the Out button in the Image Window task bar.
To display the entire image in the window:
• Select View → Zoom → Best fit from the main menu; or
Click the Full button in the Image window task bar.
To shift the area displayed in the viewer:
Select View → Zoom → Pan Image from the main menu; or
Right-click in the image and select Pan Image from the shortcut
menu.
2. Click on the image and drag to display the area of interest.
1.
You can also use the horizontal and vertical sliders to move the image.
ADJUSTING BRIGHTNESS AND CONTRAST
You can adjust the brightness and contrast to make features easier to
see.
To adjust the brightness and contrast:
1.
Select Edit → Adjust Image Brightness and Contrast... from
the main menu; or
Right-click in the image and select Adjust Image Brightness
and Contrast... from the shortcut menu.
The Brightness and Contrast dialog box opens (Figure 9.73).
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Figure 9.73
Brightness and Contrast dialog box
Adjust the sliders for Brightness and Contrast; or
Enter values in the Brightness and Contrast boxes.
You can enter values between ±1000 in the boxes
3. Click OK.
2.
Chapter
10
Gene Expression Analysis
Chapter
10
225
Gene Expression Analysis
The Expression Analysis algorithm analyzes cell intensity data from
GeneChip® expression arrays (Figure 10.1).
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 10.1
Assay & analysis flow chart
This chapter explains how to:
• Perform single-array or comparison array expression analysis.
• View the expression probe analysis data in graphical or tabular
format in the Expression Analysis window (EAW).
• Generate the following types of reports:
- Expression reports
- Grid Reports
This chapter contains the following sections:
• Overview of Expression Analysis (see below)
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• Expression Analysis Settings (see page 231)
• Single-Array Expression Analysis (see page 232)
• Comparison Expression Analysis (see page 235)
• Expression Analysis Tabular Data (see page 242)
• Expression Analysis Measured Images (see page 256)
• Expression Analysis Graphs (see page 259)
• Expression Report (see page 283)
Overview of Expression Analysis
There are two different types of expression analysis available in GCOS:
• Single-Array Expression Analysis (see below)
• Comparison Expression Analysis of an Experiment & Baseline (see
page 229)
SINGLE-ARRAY EXPRESSION ANALYSIS
A single-array expression analysis examines the cell intensity data
from one experiment (GeneChip® probe array). For each transcript
represented on the probe array, the expression algorithm computes
the:
• Detection call (present, absent, or marginal (unable to call the
transcript present or absent), or no call)
• Detection p-value
• Signal (background-subtracted and adjusted for noise)
• Stat Pairs
• Stat Pairs Used
GCOS saves the probe analysis or chip data.
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To run a single-array analysis (Figure 10.2):
Confirm the defaults or specify new values in the Expression
Analysis Settings dialog box
2. In the data tree, select the cell intensity data for the analysis.
1.
3.
Analyze the cell intensity data and view the probe analysis data in
the Expression Analysis window (EAW).
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1. Expression Analysis Settings
In the Settings shortcut bar, click the
shortcut button to open the Expression
Analysis Settings dialog box. Confirm or
specify new analysis settings. Do not
choose Use Baseline Comparison File
option.
2. Select & Analyze Cell Intensity Data
In the data tree, right-click the cell
intensity data and select Analyze from
the shortcut menu.
3. View Probe
Analysis Data
Expression Analysis
window (EAW)
displays single-array
probe analysis data.
Figure 10.2
Single-array expression analysis
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COMPARISON EXPRESSION ANALYSIS OF AN EXPERIMENT & BASELINE
A comparison analysis compares the cell intensities of the same probe
set on two different probe arrays (an experiment and baseline of the
same probe array type) to determine the relative change in the
expression level of a transcript.
For each transcript represented on the probe array, the expression
algorithm computes the:
• Change call (increase, marginal increase, no change, marginal
decrease, decrease) or no call
• Change Detection p-value
• Signal Log Ratio (background-subtracted and adjusted for noise)
• Signal Log Ratio Low
• Signal Log Ratio high
• Stat Common Pairs
GCOS saves the probe analysis data.
To run a comparison analysis (Figure 10.3):
Select the baseline probe analysis data.
2. Confirm the default expression analysis settings or specify new
values.
3. Select the experiment cell intensity data from the data tree.
4. Analyze the experiment cell intensity data and view the
comparison probe analysis data in the EAW.
1.
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Comparison Array Expression Analysis Compares an Experiment & Baseline
1. Select the baseline data:
In the Settings shortcut bar, click the
shortcut button to open the
Expression Analysis Settings dialog box.
Choose the Use Baseline Comparison
Data option. Click Browse to select the
baseline probe analysis data.
2. Expression Analysis Settings
In the Expression Analysis Settings
dialog box. Confirm or specify new
analysis settings.
3. Select & Analyze Cell Intensity Data
In the data tree, right-click the cell
intensity data and select Analyze from
the shortcut menu.
4. View Probe Analysis
Data
Expression Analysis
window (EAW)
displays comparison
analysis output.
Figure 10.3
Comparison expression analysis of an experiment and baseline
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Expression Analysis Settings
The Statistical Expression algorithm relies on the expression analysis
settings to derive biologically meaningful results from the
hybridization intensity data. The Expression Analysis Settings dialog
box (Figure 10.4) displays:
• The type of expression probe array for the analysis
• A scaling or normalization factor (for more information, see
Appendix F, Expression Algorithm, Expression Analysis Metrics &
Settings, on page 627)
• The probe mask definition (for more information, see Appendix F,
Expression Algorithm, Expression Analysis Metrics & Settings, on
page 627)
• The baseline data selected for a comparison analysis
• The user-modifiable parameters of the expression analysis
algorithm (for more information, see Appendix F, Expression
Algorithm, Expression Analysis Metrics & Settings, on page 627)
Figure 10.4
Expression Analysis Settings dialog box, Baseline tab
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Before running a single-array or comparison analysis, confirm the
defaults or specify new values for the expression analysis settings.
To open the Expression Analysis Settings dialog box (Figure 10.4),
click Expression
in the Settings shortcut bar.
2. Click a tab to view each type of setting. For more information
about the settings and how to change them, see Expression Analysis
Settings, on page 644.
The expression analysis settings are saved on a per user basis.
Changes made by one user (identified by the logon name) do not
affect the settings of other users.
1.
To compare the probe analysis data of several experiments, scale
the experiments to the same target intensity using the All Probe
Sets or Selected Probe Sets scaling option. See Scaling Tab, on
page 645.
Single-Array Expression Analysis
A single-array expression analysis analyzes the cell intensity data of a
GeneChip® expression probe array. For each transcript represented on
the probe array, the algorithm computes a Detection call, Detection pvalue, and Signal.
An expression analysis run from the data tree, menu bar, toolbar,
or workflow monitor uses the expression analysis settings in the
Expression Analysis Settings dialog box. The userset specified
during experiment setup is not applied. For more information on
usersets, see Userset Tab, on page 415.
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1.
233
Open the Expression Analysis Settings dialog box (Figure 10.4),
and:
Select the probe array type for the baseline from the Probe
Array Type drop-down list.
B. Click the Baseline tab and confirm that the Use Baseline
Comparison File option is not chosen.
A.
C.
2.
Confirm or change the other expression analysis settings as
desired.
To analyze cell intensity data, do one of the following:
- In the data tree, right-click the cell intensity data name (or
image data name), then click Analyze in the shortcut menu
that appears.
- Select File → Analyze from the menu bar and choose the cell
intensity data that you want to analyze from the Analyze
dialog box that appears.
- If the cell intensity data or image data is open, click the
Analyze ; or
Select Run → Analysis from the menu bar.
The Save Results As dialog box appears (if chosen as a default
option, see Analysis Settings, on page 335) and displays the probe
analysis data default name (same as the experiment name specified
during experiment setup) (Figure 10.5).
Figure 10.5
Save Results As dialog box
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3.
If an analysis was previously run and you want to save the current
results without overwriting the previous results, enter a new name
in the Save Results As dialog box.
4.
Click OK.
This closes the Save As dialog box and runs the single-array
analysis.
The Expression Analysis Settings dialog box appears next if chosen
as a default option. For more information on this default setting,
see Analysis Settings, on page 335.
When the analysis is finished, the Expression Analysis window
(EAW) displays the probe analysis data (Figure 10.6).
The status log (Figure 10.6) displays:
- the name of the probe analysis data
- the location of the probe analysis data
- a message indicating when the analysis is completed
If the status log is not displayed, click the Status Log button
or select View → Status Bar from the menu bar.
If the EAW is already open, the results are added to the open
window and it may be necessary to use the scrollbars at the bottom
and right side of the EAW to see the newly added results.
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Data
tree
EAW
Shortcut
bar
Status
log
Figure 10.6
Expression Analysis Window (EAW), pivot tab, single-array analysis data
Comparison Expression Analysis
A comparison expression analysis compares the cell intensity data of an
experiment to a baseline GeneChip® expression probe array (of the
same probe array type). The comparison analysis identifies the relative
change in the expression level of each transcript represented on the
probe array.
For each transcript represented on the array, the Statistical Expression
algorithm computes a Change call, Change p-value, Signal Log Ratio,
Signal Log Ratio low, and Signal Log Ratio high.
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A single-array analysis of the baseline must be run prior to running
a comparison analysis of the experiment and baseline.
Selecting the Baseline
1.
Open the Expression Analysis Settings dialog box (Figure 10.7)
(click Expression
in the Settings shortcut bar).
2.
Select the probe array type for the baseline from the Probe Array
Type drop-down list.
Figure 10.7
Expression Analysis Settings dialog box
3.
Click the Baseline tab and choose the Use Baseline Comparison
File option.
4.
Click Browse.
The Open dialog box appears (Figure 10.8).
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Figure 10.8
Open dialog box
5.
Select the baseline data and click OK.
Running the Comparison Analysis
1.
To run the comparison analysis of an experiment and baseline, do
one of the following:
- In the data tree, right-click the experiment cell intensity data
or image, and click Analyze in the shortcut menu that
appears.
- Select File → Analysis from the menu bar and choose the
experiment cell intensity data from the Analyze dialog box
that appears.
- If the cell intensity data or image is open, click the Analyze
button ; or
Select Run → Analysis from the menu bar.
The Save Results As dialog box appears (if chosen as a default
option, see Analysis Settings, on page 335) and displays the default
name for the probe analysis data (same as the experiment name
specified during experiment setup) (Figure 10.9).
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Figure 10.9
Save Results As dialog box
2.
Enter a new name in the Save Results As dialog box if an analysis
was previously run and you want to save the current results
without overwriting the previous results. Click OK.
The Expression Analysis Settings dialog box appears next if
chosen as a default option (Figure 10.10). For more information on
this default setting, see Analysis Settings, on page 335.
Figure 10.10
Expression Analysis Settings dialog box, baseline tab
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3.
239
If the Expression Analysis Settings dialog box appears, review and
confirm the settings for the probe array type and baseline data:
In the Baseline tab, select the probe array type for the baseline
from the Probe Array Type drop-down list (Figure 10.10).
B. Choose the Use Baseline Comparison Data option, then click
Browse
The Open dialog box appears (Figure 10.11).
A.
Figure 10.11
Open dialog box
C.
Double-click the baseline data; or
Click the baseline data, then click Open or OK.
The Expression Analysis Settings dialog box displays the
selected baseline data (.chp) (Figure 10.12).
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Figure 10.12
Expression Analysis Settings, baseline tab displays the baseline data for the
comparison analysis
4.
In the Expression Analysis Settings dialog box (Figure 10.12),
click the normalization tab and specify a normalization option for
the experimental data.
You need only specify a normalization option for the experiment,
not the baseline. You may use the scaling option instead of the
normalization option. If you use the scaling option, scale both the
experiment and the baseline. For more details on normalization and
scaling, see Appendix F, Expression Algorithm, Expression Analysis
Metrics & Settings, on page 627.
5.
Confirm or specify other probe array analysis parameters as desired.
For more details on the parameters, see Appendix F, Expression
Algorithm, Expression Analysis Metrics & Settings, on page 627.
6.
Click OK.
The Expression Analysis Settings dialog box closes and the
comparison analysis runs.
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When the analysis is finished, the Expression Analysis window
(EAW) displays the probe analysis data (Figure 10.13).
The status log (Figure 10.13) displays:
- the name of the probe analysis data
- the location of the probe analysis data
- a message indicating when the analysis is completed
If the status log is not displayed, click the Status Log button
or select View → Status Bar from the menu bar.
If the EAW is already open, the results are added to the open
window and it may be necessary to use the scrollbars at the bottom
and right side of the EAW to see the newly added results.
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Figure 10.13
Expression Analysis Window (EAW), comparison probe analysis data, pivot tab
Expression Analysis Tabular Data
The Expression Analysis window (EAW) has three tables that display
the tabular and graphic analysis output for gene expression assays:
• Analysis information table (see page 243)
• Metrics table (see page 245)
• Pivot table (see page 249)
The EAW opens after you complete an expression analysis or when
you open expression probe analysis data.
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You can open more than one set of probe analysis data in the EAW.
Use the EAW scroll bars to view all of the results. A second toolbar
and additional menu bar commands are available in the EAW (see
Appendix I, Toolbars, Hot Keys, & Windowpanes, on page 695).
The tabular data display is described further in:
• Analysis Information Table (see below)
• Metrics Table (see page 245)
• Pivot Table (see page 249)
• Finding Probe Set Information (see page 253)
• Sorting Probe Set Information (see page 254)
• Reordering or Removing Probe Set Information (see page 255)
• Hiding Probe Set Information (see page 256)
ANALYSIS INFORMATION TABLE
The analysis information table (Figure 10.14) displays experiment and
sample information entered during experiment setup, values for usermodifiable expression analysis algorithm settings, and other
information. Each column in the analysis information table represents
one analysis (probe array).
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Figure 10.14
Expression Analysis window, analysis information table
Exporting Analysis Information
You can export the data in the analysis information table to a tab
delimited text file (.txt) or Microsoft® Excel file (.xls).
To export the data:
1.
If it is not already open, open the EAW (in the data tree, doubleclick the probe analysis data that you want to export).
Click the Analysis Information tab.
3. To export a user-selected portion of the data table, highlight the
cells of interest.
2.
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4.
245
Click the Save button ; or
Select File → Save As from the menu bar.
The Save As dialog box appears (Figure 10.15).
Figure 10.15
Save As dialog box
5.
Choose a Save Option:
- Save All exports all of the analysis information table data to
the text file.
- Save Selected exports only the user-selected portion of the
analysis information table to the text file.
Enter a name for the text file and confirm or select another
directory for the text file.
7. Click Save to export the experiment information table or selected
experiment data.
6.
METRICS TABLE
The metrics table (Figure 10.16) displays data for each probe set in the
selected probe analysis data (Table 10.1). For definitions of the
Statistical expression metrics see Expression Analysis Metrics, on
page 636.
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Table 10.1
Statistical expression algorithm metrics
Single-Array Analysis
Comparison Analysis
Stat Pairs
Stat Common pairs
Stat Pairs Used
Signal Log Ratio
Signal
Signal Log Ratio low
Detection
Signal Log Ratio high
Detection p-value
Change
Change p-value
Figure 10.16
Expression Analysis window, metrics tab, single-array probe analysis data for
experiments N002 and N004
Exporting Metrics Data
You can export metrics data and the associated analysis information as
a text file (.txt) or Microsoft® Excel file (.xls).
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Setting Metrics Export Preferences
Click the Analysis Options button .
The Analysis Options dialog box appears (Figure 10.17).
2. Click the metrics tab to view export preferences.
1.
Figure 10.17
Analysis Options, Metrics tab
Choose the Save Analysis Info option to include the analysis
information with the metrics data for export.
4. Choose the Save All Metric Results option to view the save
preferences:
- The Save all analyses to one file option exports the analysis
information and metrics data for all analyses in the EAW to
one text file (.txt).
- The Save each analysis to a separate file option exports the
analysis information and metrics data for each analysis in the
EAW to a separate text file.
3.
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The save preferences set in the metrics tab do not affect the save
function in the Pivot or Analysis Information tab in the EAW.
5.
Click OK to close the Analysis Options dialog box.
Exporting Metrics Data
If it is not already open, open the EAW (in the data tree, doubleclick the probe analysis data of interest), then click the Metrics tab.
2. To export:
1.
- All of the metrics table, click the Save button ; or
Select File → Save As from the menu bar.
- A selected portion of the metrics table, highlight the rows of
interest, then click the Save button ; or
Select File → Save As from the menu bar.
Do not choose the Save All Metric Results option (Figure 10.17) if
you want to save selected results.
The Save As dialog box appears (Figure 10.18).
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Figure 10.18
Save As dialog box
Enter a name for the text file and confirm or select another
directory for the text file.
4. Click Save to export the metrics data according to the preferences
set in the Analysis Options (Metrics tab) (Figure 10.17).
3.
PIVOT TABLE
To view the pivot table:
• Open probe analysis data (double-click the data in the data tree).
• Click the Pivot tab in the EAW.
Each row in the pivot table (Figure 10.19) begins with a probe set
name and each set of columns displays the results from one probe
analysis. The pivot table displays probe analysis data and descriptions
for each transcript represented on the probe array.
If several sets of probe analysis data from the same probe array type are
open in the EAW, each row of the pivot table displays the data for one
probe set from the different experiments. The pivot table is organized
so that probe analysis data from different experiments may be easily
compared.
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Figure 10.19
Expression Analysis window (EAW), pivot table, single-array probe analysis data
for experiments N002 and N006
Pivot Table Display Options
Single-array or comparison analysis output
You can select the types of single-array or comparison analysis output
(columns) displayed in the pivot table.
1.
Click the Analysis Options button .; or
Select Analysis → Options from the menu bar.
The Analysis Options dialog box appears (Figure 10.20).
2.
Click the Pivot tab.
The pivot table includes column headers for the items selected in
the Analysis Options dialog box. You can also view these items by
selecting View → Pivot Data from the menu bar.
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Select the output for
display in the Pivot table.
Figure 10.20
Analysis Options dialog box, Pivot tab
The pivot table can also display probe analysis data for experiments
analyzed using the Empirical expression analysis algorithm (in
Microarray Suite versions lower than 5.0).
3.
Click an unchecked item to add it to the pivot table or click a
checked item to remove it from the table.
4.
To reorder an experiment result column in the pivot table, use the
drag-and-drop method to move the column header in the table.
Probe Set Descriptions
To view probe set descriptions, do either of the following:
• Scroll to the Descriptions (far right column) in the pivot table.
• Double-click the row of interest in the pivot table.
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The Description dialog box is displayed (Figure 10.21).
Figure 10.21
EAW, probe set Description dialog box
Obtaining Further Information
You can search for further information about a probe set at an Internet
site.
To obtain further information about a probe set in the metrics
or pivot table:
Right-click the probe set (row) of interest.
2. Select External Database → NetAffx™ (or Entrez) from the
shortcut menu that appears.
This starts the default Internet browser (for example, Microsoft®
Internet Explorer or Netscape® Communicator®) and
automatically opens the selected Internet site.
1.
Exporting the Pivot Table
You can export the pivot table as a text file (.txt) or Excel file (.xls).
If it is not already open, open the EAW (in the data tree, doubleclick the probe analysis data of interest).
2. Click the Pivot tab.
1.
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To export only a user-selected portion of the data table, highlight
the cells of interest.
4. Click the Save button
or select File → Save As from the menu
bar.
The Save As dialog box appears (Figure 10.22).
3.
Figure 10.22
Save As dialog box
5.
Choose a save option:
- Save All places all of the pivot table in the text file.
- Save Selected places only the selected pivot data in the text
file.
Enter a name for the text file and confirm or select another
directory for the text file.
7. Click Save to export the pivot table or selected pivot data.
6.
FINDING PROBE SET INFORMATION
You can perform text searches in the EAW.
1.
To start a text search, do one of the following:
- Click the Find button
.
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- Select Edit → Find from the menu bar.
- Right-click the metrics or pivot table and select Find in the
shortcut menu that appears.
The Find dialog box appears (Figure 10.23).
Figure 10.23
Find dialog box
Enter the text string for the search (up to 256 alphanumeric
characters).
3. Choose the Match or Direction search option, then click Find
Next. Click Find Next again to continue the search.
2.
The Find command finds all strings that match the text string for the
search. For example, using the Find command to search for the text
string biob would find AFFX-BioB-5 as well as other occurrences of
BioB.
SORTING PROBE SET INFORMATION
You can sort the metrics or pivot table by any category of data
displayed in the table.
Single Column Sort
In the EAW, click the Metrics or Pivot tab.
2. Right-click the column header of interest and click Sort
Ascending or Sort Descending in the shortcut menu that
appears.
1.
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Multiple Column Sort
In the EAW, click the Metrics or Pivot tab.
2. Click the Sort button
; or
Select Edit → Sort from the menu bar.
The Sort dialog box appears (Figure 10.24).
1.
Figure 10.24
Sort dialog box
Select the desired sort category from the first (top) drop-down list
and choose an ascending or descending sort order.
Up to three additional sort categories may be specified.
4. Click OK when finished specifying the sort.
The sort category and order are displayed at the bottom of the
EAW.
3.
REORDERING OR REMOVING PROBE SET INFORMATION
Reordering Columns in the Metrics or Pivot Table
In the Metrics or Pivot tab, click the column header of interest.
2. Use the drag-and-drop method to move the column to a new
position in the table.
1.
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Reordering Rows in the Metrics or Pivot Table
Use the Edit commands in the menu bar to remove or reorder tabular
data in the metrics or pivot table:
Edit → Move Selected to Top Moves a selected row(s) to the top of the metric or
pivot table.
Edit → Remove Analyses
Edit → Select All
When the pivot table contains only one analysis,
removes the analysis from the table (equivalent to
closing the probe analysis data). When the pivot table
includes more than one analysis, this displays an
Open dialog box that enables you to select the
analyses you want to remove from the table.
Highlights all rows in the metric or pivot table.
HIDING PROBE SET INFORMATION
You can hide tabular data in the metrics or pivot table. Use the View
commands in the menu bar to hide (unhide) selected rows or all of the
tabular data.
Alternatively, right-click the metrics or pivot table to display a
shortcut menu of hide commands:
View → Hide Selected
View → Hide Unselected
View → Unhide All
Hides the currently selected row(s) in the metrics or pivot
table. The status bar at the bottom of the EAW displays the
remaining number of rows in the table.
Hides all unselected rows in the metrics or pivot table. The
status bar at the bottom of the EAW displays the
remaining number of rows in the data table.
Displays all previously hidden rows at the bottom of the
data table.
Expression Analysis Measured Images
A measured image displays the probe set hybridization intensity data
(from the image data).
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Measured images are displayed in the following sections:
• Displaying Measured Images (see below)
• Clearing Measured Images (see page 258)
DISPLAYING MEASURED IMAGES
To display measured images:
1.
Click the desired probe set name(s) in the metrics or pivot table.
To select adjacent probe set names, press and hold the Shift key
and click the first and last probe set name in the selection. To select
non-adjacent probe set names, press and hold the Ctrl key while
you click the desired names.
2.
Click the Image button ; or
Select Graphs → Measured Images from the menu bar.
The graph pane (Intensity tab) opens and displays the measured
image and the intensity signal range for the selected probe set
(Figure 10.25).
When an additional image is created, the graph pane
automatically scrolls to the new image. Use the scroll bar to view
all of the measured images created during a session. For
information about resizing the graph pane see Working with
Windowpanes & Columns, on page 705.
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Probe set
measured
images in
the graph
pane
Figure 10.25
EAW, measured images in the graph pane (top)
CLEARING MEASURED IMAGES
You can remove all or selected images from the graph pane.
To remove all measured images from the graph pane, right-click
the graph pane and select Clear All Graphs from the shortcut
menu that appears; or
Select Graph → Clear All Graphs from the menu bar.
2. To remove selected images from the graph pane:
1.
Double-click the measured image.
B. Right-click the image and select Clear Selected Graphs from
the shortcut menu that appears; or
Select Graph → Clear Selected Graphs from the menu bar.
A.
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Expression Analysis Graphs
GCOS plots three types of expression analysis graphs (Table 10.2).
The graphs are displayed in the graph pane that appears at the top of
the EAW (Figure 10.26).
Table 10.2
Expression analysis graphs
Expression
Graph Type
Plots...
Scatter
A user-specified metric for all probe sets from two experiments
(of the same probe array type) using a traditional scatter plot.
For more information, see Scatter Graph, on page 260.
Series
A user-specified metric for each probe set on the array in a bar
or line graph format. For more information, see Series Graph,
on page 274.
Intensity
The intensities of the probe pairs in a probe set using a bar
graph format. For more information, see Intensity Bar Graph,
on page 279.
The graph pane has three tabs:
• Scatter Graph (see page 260)
• Series Graph (see page 274)
• Intensity (see page 279)
Click the graph pane tabs to toggle the display among the different
graph types. For information about resizing the graph pane see
Working with Windowpanes & Columns, on page 705.
The intensity graph and images functions are unavailable until a
probe set(s) is highlighted in the metrics or pivot table.
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Scatter graph in
the graph pane
Pivot
table
Figure 10.26
Expression Analysis window (EAW), Scatter graph tab of the graph pane (top) and Pivot tab (bottom)
SCATTER GRAPH
The scatter graph plots user-selected expression data for all probe sets
from one or more pairs of analyses using a traditional scatter plot
(Figure 10.26). Each point in the scatter graph represents a probe set
common to both experiments and is defined by the intersection of the
analysis result value on the x and y axes for the common probe set. The
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scatter graph displays fold change lines (four pairs) that help identify
probe sets in the comparison that change expression levels.
Plotting a Scatter Graph
1.
Click the Scatter graph button ; or
Select Graph → Scatter Correlation Graph from the menu bar.
The Scatter Graph dialog box displays the pivot table columns
available for the scatter graph (Figure 10.27).
For the scatter plot, select pairs of analyses that are derived from
the same probe array type. The order of the analyses is critical. For
example, the analyses from a multiple probe array set must be
ordered identically along the x and y-axes since the scatter graph
compares the first set of analysis outputs on the x-axis with the first
set of analysis outputs on the y-axis (and so forth). If the analysis
outputs are not in identical order, many probe sets will not be
compared and plotted (only the probe sets in common such as the
controls).
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This box shows the
pivot table columns
available for the
scatter graph
Figure 10.27
Scatter graph dialog box
2.
To select a column for the x-axis, do either of the following:
- Use the drag-and-drop method to move the column name
from the Available Columns box to the Select X Axis
Columns box (Figure 10.27).
- Highlight the column name in the Available Columns box,
then click the down arrow
(on the left side) to place the
column in the Select X Axis Columns box.
3.
To select a column for the y-axis, do either of the following:
- Use the drag-and-drop method to move the column name
from the Available Columns box to the Select Y Axis
Columns box (Figure 10.27).
- Highlight the column name in the Available Columns box
and click the down arrow
(on the right side) to place the
column in the Select Y Axis Columns box.
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To change the order of columns, do either of the following:
- Use the drag-and-drop method to move the column to the
desired location in the list.
- Highlight the column name, then use the up
and down
arrows located to the inside of the Select Axis Columns
boxes.
To select linear scaling, remove the check mark from the Log Scale
check box.
Logarithmic scaling is the default.
6. Click OK to generate the scatter graph.
The graph pane (Scatter Graph tab) displays the scatter graph
(Figure 10.26).
5.
Working with the Scatter Graph
Right-click the scatter graph to display a shortcut menu of commands
that include:
Points
Displays the absolute call combinations and the color assigned to
each. The scatter graph displays the check marked items. Click an
item to remove or add a check mark. The scatter graph is
immediately updated.
Copy Graph
Copies the Scatter graph to the system clipboard.
Close Graph
Pane
Closes the graph pane. Graphs created during the session are not
saved.
Full Out Zoom
Restores the graph to the original magnification view.
Redraw Graph
Redraws the scatter graph so that it plots only the points that
correspond to rows displayed in the pivot table. Points that
correspond to hidden rows are not plotted.
Select
Highlighted
Points
Selects rows in the Pivot and Metric tables that correspond to points
selected (roped) in the Scatter graph.
Options
Displays the Analysis Options dialog box.
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Magnifying the Graph
Press and hold the Shift key while you use the click-and-drag
method to draw a rectangle over the graph area of interest
(Figure 10.28).
2. Release the mouse key.
This magnifies the area selected by the rectangle (Figure 10.29).
1.
3.
To zoom out and restore the graph, right-click the graph and select
Full Out Zoom from the shortcut menu that appears.
Figure 10.28
Scatter graph, rectangle selects an area to magnify
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Figure 10.29
Magnified area in the scatter graph
Displaying Probe Set and Gene Information
1.
Click a point in the scatter graph.
This displays the probe set name, parameter value, detection call,
and a brief description of the probe set (Figure 10.30). The
corresponding row in the pivot table is highlighted.
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Database drop-down list
Figure 10.30
Scatter graph, click a point to display corresponding probe set and gene
information
2.
To obtain further gene information, select a database from the
drop-down list and click Info.
The Internet browser window opens and displays information for
the selected gene (Figure 10.31).
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Figure 10.31
Internet browser window
Selecting Points in the Scatter Graph
1.
Click the Lasso button ; or
Select Graph → Lasso Points from the menu bar.
The mouse pointer changes to a cross hairs (+) when it is
positioned over the scatter graph
2.
To rope points of interest, position the cross hairs near the group
of points, then do either of the following:
- Use the click-and-drag method to draw a circle around the
points, then release the mouse button near the starting point.
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- Click the mouse, move it to draw a line segment, then click
the mouse again to start drawing a new line segment. Repeat
until you return the cross hairs to the starting point and the
line segments enclose the points of interest.
This completes the lasso operation (Figure 10.32).
The scatter graph displays the selected points in orange. The
metrics and pivot tables highlight the corresponding probe sets.
Press the Esc key to cancel the lasso operation.
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Figure 10.32
Roping points in the scatter graph highlights the corresponding probe set rows
in the metrics and pivot tables
After you select points in the scatter graph, hide the unselected rows
in the pivot table, then use the Redraw Graph command to display only
the selected points in the scatter graph.
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Hiding Points in the Scatter Graph
You can hide points in the scatter graph according to detection or
Change call (if the scatter graph points are color coded using the Color
by Detection/Absolute Call or Color by Change/Difference Call
option, see Point Options, on page 271.
1.
Right-click the scatter graph and select Points from the shortcut
menu that appears.
This displays a key for the scatter graph point colors
(Figure 10.33).
Figure 10.33
Scatter graph shortcut menu, point color combinations for detection calls
2.
Click a point color combination to remove (or add) a check mark.
This hides (unhides) the selected points in the scatter graph.
Scatter Graph Options
You can modify some display features of the scatter graph. The
Analysis Options dialog box displays the user-modifiable features
(Figure 10.34).
1.
To open the Analysis Options dialog box, do one of the following:
- Click the Options button .
- Right-click the scatter graph and select Options from the
shortcut menu that appears.
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- Select Analysis → Options from the menu bar.
The Analysis Options dialog box appears (Figure 10.34).
2.
Click the Scatter Graph tab.
Figure 10.34
Analysis Options, Scatter Graph tab
Point Options
Point Size
Determines the size of the graph points. Enter a larger point size
number for easier viewing, but use a smaller point size for high
resolution graphs.
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Color by Detection/ Displays the graph points using the colors assigned to the singleAbsolute Call
array call combination of the x and y-axis analyses. There are
nine possible call combinations:
Absent in Y
Marginal in Y Present in Y
A-A
M-A
A-P
Marginal in X M-A
M-M
M-P
P-M
P-P
Absent in X
Present in X
P-A
Color coding the combinations can help quickly determine whether
a highly expressed gene in one experiment was present or absent
in another experiment.
If the call is No Call in either analysis, the point is displayed using
the No Call Point Color (the default is black).
Color by Change/
Difference Call
Displays the data points using the colors assigned to the
comparison analysis call of the y-axis analysis. There are five
possible calls: Decrease (D), Marginal Decrease (MD), No
Change (NC), Marginal Increase (MI), and Increase (I).
Use Point Color
Displays points using the color assigned to the Point Color.
Fold Change Lines
The default fold change lines are defined in pairs: y = 2x and y = 1/2x,
y = 3x and y = 1/3x, y = 10x and y = 1/10 x, y = 30x and y = 1/30x.
The fold change lines (four pairs) are drawn using the values entered
in the edit boxes. Only integer values may be entered. Removing a
check mark turns off the display of that pair of fold change lines.
Colors
You can change the colors assigned to the:
• single-array analysis call categories
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• comparison analysis call categories
• scatter graph points
• graph background
• selected (roped) scatter graph points
• fold change lines
1.
In the Analysis Options dialog box (Figure 10.34), click the color
square associated with the item you want to change.
This displays the color palette (Figure 10.35).
Custom color
Luminosity
scale
Figure 10.35
Color palette
To select a predefined color, click one of the basic colors.
3. To define a custom color, click Define Custom Colors, then use
the click-and-drag method to move the cross hairs in the custom
color field. Adjust the color brightness using the luminosity scale
to the right. When finished, click Add to Custom Colors to
apply the color.
4. Click OK to close the color palette.
The color choices are saved on a per user basis.
2.
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Defaults
Click Defaults to return all analysis option settings to the factory set
defaults.
SERIES GRAPH
The series graph plots a line or bar graph of user-selected expression
data for all analyses or for all probe sets of analyses open in the EAW
(Figure 10.36 and Figure 10.37). The line graph format is the default.
Hidden probe sets are not included in the series graph.
Figure 10.36
Series line graph, signal
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Figure 10.37
Series bar graph, signal
Plotting a Series Graph
1.
Click the Series Graph button ; or
Select Graph → Series Graph from the menu bar.
The Series Graph dialog box appears (Figure 10.38).
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Figure 10.38
Series Graph dialog box
2.
Select the pivot table columns for the series graph.
This generates the series line graph for the probe sets displayed in
the data tables (Figure 10.36).
The line graph format is the default. For information on how to
change the bar graph format, see Series Graph Options, on page 277.
Working with the Series Graph
Place the mouse arrow over a probe set name, data point, or bar to
view a pop-up tool tip that displays the analysis or probe set name
and parameter value.
2. Right-click the series graph to display a shortcut menu of
commands that include:
1.
Copy Graph
Copies the graph to the system clipboard.
Close Graph
Pane
Closes the graph pane (graphs created during the session are not
saved).
Options
Displays the Analysis Options dialog box.
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Series Graph Options
Some display features of the series graph may be modified. The
Analysis Options dialog box displays the user-modifiable features
(Figure 10.39).
1.
To open the Analysis Options dialog box, do one of the following:
- Click the Options button .
- Right-click the scatter graph and select Options from the
shortcut menu that appears.
- Select Analysis → Options from the menu bar.
The Analysis Options dialog box appears (Figure 10.39)
2. Click the Series Graph tab and choose the Bar Graph or Line
Graph option.
Figure 10.39
Analysis Options, Series Graph tab
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Series Bar Graph Options
Probe Set Width (%)
Determines the graph bar width.
X-Axis Parameters Visible
The number of probe sets displayed on the x-axis within the
viewable portion of the graph.
Series Line Graph Options
X-Axis
Select Probe Sets or Columns (from the X-Axis drop-down list) for
display on the x-axis.
Point Size
Determines the size of the graph points.
X-Axis Parameters
Visible
Specifies the number of probe sets or columns displayed on the xaxis within the viewable portion of the graph.
Colors
The color of the points or background in the series line graph may be
changed.
1.
In the Analysis Options dialog box (Figure 10.39), click the Point
Color or Background color square.
This displays the color palette (Figure 10.40).
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Custom color
279
Luminosity
scale
Figure 10.40
Color palette
To select a predefined color, click one of the basic colors.
3. To define a custom color, click Define Custom Colors, then use
the click-and-drag method to move the cross hairs in the custom
color field. Adjust the color brightness using the luminosity scale
to the right. When finished, click Add to Custom Colors to
apply the color
4. Click OK to close the color palette.
The color choices are saved on a per user basis.
2.
INTENSITY BAR GRAPH
The intensity bar graph displays the intensities of the probe pairs of a
probe set in a bar graph format (Figure 10.41). The intensity bar graph
is a useful way to:
• Evaluate the relative performance of the probe pairs in a probe set.
• Determine whether an image or probe mask has been applied to a
probe pair.
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Figure 10.41
Intensity bar graph of probe set X54925_at (from experiment N004)
Plotting the Intensity Bar Graph
Highlight a row or cell in the metrics or pivot table.
2. To plot the intensity bar graph(s) for the highlighted probe set(s),
do either of the following:
1.
- Click the Intensity Bar Graph button .
- Select Graph → Intensity Bar Graph from the menu bar.
3.
If necessary, use the scroll bar to view all of the intensity bar graphs
created during a session.
Intensity Bar Graph Options
You can modify some display features of the intensity bar graph. The
Analysis Options dialog box displays the user-modifiable features
(Figure 10.42).
1.
To open the Analysis Options dialog box, do one of the following:
- click the Options button
- right-click the intensity bar graph, then click Options in the
shortcut menu that appears
- select Analysis → Options from the menu bar
The Analysis Options dialog box appears (Figure 10.42)
2.
Click the Intensity Graph tab.
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Figure 10.42
Analysis Options, Intensity Graph tab
Show Values
Choose the Show Values option to display numerical intensity values
on the intensity bar graph.
Scale
Relative to Pair
Scales each probe pair set independently. The scale for each PM and
MM pair is 0 → max (PM, MM).
Relative to Probe
Set
Scales each probe pair relative to all probe pairs of a particular probe
set. The scale is determined by all pairs of the probe set and ranges
from 0 → max (all PM/MM probe pairs in the set).
Absolute
Scales all probe pairs according to a user specified intensity range (for
example, 10 to 1000 in Figure 10.42).
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Colors
The color code specifies the colors for:
Match
Perfect match probe intensities
Mismatch
Mismatch probe intensities
Image Mask
Probe pairs included in an image mask
Probe Mask
Probe pairs included in a probe mask
Not in Average
Probe pairs excluded from the Average Difference calculation
(Empirical expression algorithm only)
To change the colors specified by the color code:
1.
Click the color square of the item you want to change (for example,
Match in Figure 10.42).
This displays the color palette (Figure 10.43).
Custom color
Luminosity
scale
Figure 10.43
Color palette
To select a predefined color, click one of the basic colors.
3. To define a custom color, click Define Custom Colors, then use
the click-and-drag method to move the cross hairs in the custom
color field. Adjust the color brightness using the luminosity scale
2.
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to the right. When finished, click Add to Custom Colors to
apply the color
4. Click OK to close the color palette.
The color choices are saved on a per user basis.
Defaults
Click Defaults to restore the factory set defaults for all intensity bar
graph options.
Clearing Intensity Bar Graphs
To remove all intensity bar graphs from the graph pane, rightclick the graph pane and select Clear All Graphs from the
shortcut menu that appears; or
Select Graph → Clear All Graphs from the menu bar.
2. To remove user-selected intensity bar graphs from the graph pane:
1.
Double-click the graph(s) you want to remove.
B. Right-click the selected graph and select Clear Selected
Graphs from the shortcut menu that appears; or
Choose Graph → Clear Selected Graphs from the menu bar.
A.
Expression Report
The expression report summarizes information about the expression
analysis settings, algorithm settings, and probe set hybridization
intensity data.
You can learn more about expression reports in the following sections:
• Generating an Expression Report (see below)
• Expression Report Components (see page 287)
• Expression Report Settings (see page 289)
• Expression Report View Options (see page 291)
• Editing an Expression Report (see page 291)
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• Saving an Expression Report (see page 292)
GENERATING AN EXPRESSION REPORT
1.
Confirm or change the user-modifiable report settings. See the
next section Expression Report Settings.
2.
To generate the report, do either of the following:
- In the data tree, right-click the probe analysis data for the
report and select Report from the shortcut menu that appears.
- Select File → Report from the menu bar, then in the Report
dialog box (Figure 10.44) that appears, double-click the probe
analysis data for the report.
Figure 10.44
Report dialog box
This displays the expression report in the main display area.
Figure 10.45 and Figure 10.46 show an example expression
report.
3. To best view the expression report:
A.
Use Arial font (10 point) (select View → Set Font from the
menu bar).
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B.
285
Set the tab stops set at 10 (select View → Set Tab Stops from
the menu bar).
A previously generated report will be overwritten. To save a
previous report, rename it and save it under the new name. See the
Saving an Expression Report, on page 292.
Figure 10.45
Expression report, comparison analysis, Statistical Expression algorithm
(page 1)
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Figure 10.46
Expression report, comparison analysis, Statistical Expression algorithm (page
2)
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EXPRESSION REPORT COMPONENTS
Statistical Expression Algorithm
Probe Pair Threshold
Alpha1 (α1)
The minimum number of probe pairs a probe set must have in
order for the probe set data to be included in the calculation of the
report statistics
The significance level for the Detection p-value in an analysis.
Alpha1 is a user-modifiable parameter that is set in the Parameters
tab of the Expression Analysis Settings. See Expression Analysis
Settings, on page 644.
If the probe set Detection p-value < alpha1, the call is present.
Alpha2 (α2)
The second significance level for the Detection p-value in an
analysis. Alpha2 is a user-modifiable parameter set in the
Parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644.
If the probe set Detection p-value ≥ alpha2, the call is absent. If
alpha1 ≤ Detection p-value < alpha2, the call is marginal.
Tau (τ)
Tau is a user-modifiable parameter that is set in the Parameters tab
of the Expression Analysis Settings See Expression Analysis Settings,
on page 644. Ideally, tau should be set to a value that is a little larger
than the median of the discrimination scores of the probe sets
whose targets are absent to avoid false detected calls.
Noise (Raw Q)
The degree of pixel-to-pixel variation among the probe cells used
to calculate the background. See Statistical Expression Algorithm, on
page 636.
Scale Factor (SF)
The scale factor specified in the Scaling tab of the Expression
Analysis Settings dialog box or computed by the algorithm. See
Expression Analysis Settings, on page 644.
TGT Value
The user-specified target signal for scaling of the experiment
probe array. The target signal is set in the Scaling tab of the
Expression Analysis Settings dialog box. See Expression Analysis
Settings, on page 644.
Norm Factor (NF)
The normalization factor specified in the Normalization tab of the
Expression Analysis Settings dialog box or computed by the
algorithm. See Expression Analysis Settings, on page 644.
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Gamma1H (γ1H)
Gamma2H (γ2H)
Gamma1L (γ1L)
Gamma2L (γ2L)
The small significance level for Change calls at high intensities.
Gamma1H is a user-modifiable parameter that is set in the
Parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644.
The large significance level for Change calls at high intensities.
Gamma2H is a user-modifiable parameter that is set in the
Parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644.
The small significance level for Change calls at low intensities.
Gamma1L is a user-modifiable parameter that is set in the
Parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644.
The large significance level for Change calls at low intensities.
Gamma2L is a user-modifiable parameter that is set in the
Parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644.
Perturbation
A user-modifiable expression algorithm parameter that is set in the
parameters tab of the Expression Analysis Settings. See Expression
Analysis Settings, on page 644. Perturbation influences the p-value
computed for a probe set in a comparison analysis.
Baseline Noise (Raw
Q)
The degree of pixel-to-pixel variation among the probe cells used
to calculate the background in the baseline probe array. See
Statistical Expression Algorithm, on page 636.
Baseline Scale Factor
(SF)
The scale factor specified for the baseline probe array in the
Scaling tab of the Expression Analysis Settings dialog box or
computed by the algorithm. See Expression Analysis Settings, on
page 644.
Background
Minimum, maximum, average, and standard deviation of the
background intensity calculated for the probe array.
Noise
The minimum, maximum, average, and standard deviation of the
noise calculated for the probe array.
Corner+
The average cell intensity for the sense probe cells used in the grid
alignment process.
Corner-
The average cell intensity of the antisense probe cells used in the
grid alignment process.
Central+
The average cell intensity for the nine probe cells that comprise
the cross at the center of a sense probe array.
Central-
The average cell intensity for the nine probe cells that comprise
the cross at the center of an antisense probe array.
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Total Probe Sets
The number of probe sets on the array that exceed the probe pair
threshold and are not called No Call.
Average Signal
The average signal for all probe sets that exceed the probe pair
threshold and are not called No Call.
Controls
The expression report includes the signal and call data for the
probe sets that correspond to the housekeeping or spike control
transcripts. Separate signal and call data are reported for the probe
pairs specific to the 5’, middle (M), and 3’ regions of the control
transcripts.
Sig(all)
The average signal for all control probe sets.
Sig(3′/5′)
For a probe set, Sig(3′)/Sig(5′).
EXPRESSION REPORT SETTINGS
The expression report has user-modifiable settings.
1.
To view the user-modifiable settings, click Settings in the
shortcut bar, then click Expression Report .
The Expression Report dialog box appears (Figure 10.47).
Figure 10.47
Expression Report dialog box
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Probe Pair Threshold
The minimum number of probe pairs a probe set must have in
order for the probe set data to be included in the calculation of
the report statistics.
Antisense Probe Sets
Choose this option for probe arrays that have antisense control
probes. (Refer to the probe array product insert.)
Sense Probe Sets
Choose this option for probe arrays that have sense control
probes. (Refer to the probe array package insert.)
Housekeeping Controls
Housekeeping controls are housekeeping gene transcripts that are
usually constitutively expressed in the sample. The transcripts serve as
endogenous controls and are useful for monitoring the quality of the
target.
The report includes the signal (Sig) for probe sets that are designed to
be specific to the 5′, middle, or 3′ portion of the transcript. These data
are informative about the reverse transcription and IVT steps in
sample preparation.
Differences greater than three fold between the Sig 3′ and Sig 5′ (Sig
3′/5′) for a housekeeping control indicate the target may be degraded
and should be prepared again.
To delete a housekeeping control from the expression report:
Double-click the probe set name.
2. Right-click probe set and select Delete from the shortcut menu
that appears.
1.
Spike Controls
Spike controls are transcripts that are added to or spiked in the sample.
These are exogenous transcripts that are useful for monitoring assay
procedures such as hybridization, washing, and staining.
To delete a spike control from the expression report:
1.
Double-click the probe set name.
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2.
291
Right-click probe set and select Delete from the shortcut menu
that appears.
Other Controls
You can choose any probe set on the array as a control. Enter the probe
set name in the Other Controls box. The expression report includes
the signal and detection call for user-specified controls.
EXPRESSION REPORT VIEW OPTIONS
Find Feature
The Find feature searches the report.
1.
Click the Find button
or select Edit → Find from the menu
bar.
The Find dialog box appears (Figure 10.48).
Figure 10.48
Find dialog box
Enter the text for the search (up to 256 alphanumeric characters
including spaces) in the Find what box, then click Find Next to
view the first search result.
3. Click Find Next or the Find Next button
to view each
successive search result.
2.
EDITING AN EXPRESSION REPORT
Edit commands for the expression report are available in the:
• Edit menu bar
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• Report window toolbar
• Shortcut menu (right-click the report)
Replace Feature
The replace feature performs a text search and replaces the search item
with specified text.
1.
Select Edit → Replace from the menu bar.
The Replace dialog box appears (Figure 10.49).
Figure 10.49
Replace dialog box
Enter the text for the search in the Find what box and enter the
replacement text in the Replace with box.
3. Click Find Next to begin the search, then click Replace to replace
the search item with the specified text. Repeat to find and replace
successive instances of the search item; or
Click Replace All to find and replace all occurrences of the search
item in the report.
2.
SAVING AN EXPRESSION REPORT
When GCOS generates a report for expression probe analysis data, it
overwrites a previously generated report. To prevent a previous report
from being overwritten, save it under a new name.
1.
To open the report that you want to save under a new name, click
the Open button .
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The Open dialog box appears (Figure 10.50).
Figure 10.50
Open dialog box
Double-click the report name.
The report is displayed.
3. Select File → Save As from the menu bar.
The Save As dialog box appears (Figure 10.51).
2.
Figure 10.51
Save As dialog box
4.
Click the report to be saved, then enter a new name for the report
in the File name box.
5.
Click Save.
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Chapter
11
Batch Analysis
Chapter
11
297
Batch Analysis
Batch analysis is a convenient way to analyze the cell intensity data
from many different experiments and to generate probe analysis data
with unattended operation.
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 11.1
Assay & analysis flow chart
This chapter contains the following sections:
• Opening the Batch Analysis Window (see below)
• Selecting Data for Batch Analysis (see page 298)
• Renaming Results from Batch Analysis (see page 306)
• Removing Data from the Batch Analysis Window (see page 308)
• Running a Batch Analysis (see page 309)
• Exporting a Batch File (see page 309)
• Importing a Batch File (see page 310)
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Opening the Batch Analysis Window
To open the Batch Analysis window:
• In the GeneChip Software shortcut bar, click Batch Analysis
• Select Run → Batch Analysis from the menu bar.
The Batch Analysis window opens (Figure 11.2).
Figure 11.2
Batch Analysis window
Selecting Data for Batch Analysis
You may select cell intensity data or probe analysis data for batch
analysis. If you select cell intensity data, GCOS automatically places
the parent cell intensity data and baseline probe analysis data (if
applicable) in the Batch Analysis window.
Batch analysis will overwrite previous probe analysis data.
.
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299
Using the Drag-and-Drop Method
1.
In the data tree, select the cell intensity data or probe analysis data
that you want to analyze.
To select adjacent items, press and hold the Shift key while you
click the first and last item in the selection. To select non-adjacent
items, press and hold the Ctrl key while you click the items.
2.
Drag the selected data from the data tree to the Batch Analysis
window (Figure 11.3).
Data tree
Shortcut bar
Figure 11.3
Batch Analysis window
Batch analysis window
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Using the Toolbar or Menu Commands
1.
Click the Add button
or select Edit → Add Item from the
menu bar.
The Add Cell/Chip Data dialog box appears (Figure 11.4).
Click Details
to display experiment and sample information
for the cell intensity or probe analysis data.
Figure 11.4
Add Cell/Chip Data dialog box
2.
To filter the data in the Add Cell/Chip Data dialog box:
Click Filter.
The advanced filter appears (Figure 11.5).
B. Make selections from the drop-down lists.
C. Click Apply.
A.
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Figure 11.5
Add Cell/Chip Data dialog box, advanced filter
3.
Select the data for the batch analysis, then click OK.
To select adjacent items, press and hold the Shift key while you
click the first and last item in the selection. To select non-adjacent
items, press and hold the Ctrl key while you click the items.
The selected cell intensity data are added to the Batch Analysis
window (Figure 11.6).
Batch analysis will overwrite previous probe analysis data.
The Batch Analysis window displays previously analyzed cell
intensity data in red to indicate that the existing probe analysis
data will be overwritten. To reanalyze experiments without
overwriting existing probe analysis data, specify a different name
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for the .chp from the batch analysis. See Renaming Results from Batch
Analysis, on page 306.
Figure 11.6
Batch Analysis window, cell intensity data (.cel) selected for batch analysis
You can also use the Batch Analysis window for:
• Selecting a Userset for Expression Analysis (see below)
• Selecting a Baseline for a Comparison Expression Analysis (see page 303)
SELECTING A USERSET FOR EXPRESSION ANALYSIS
A userset specifies the expression analysis settings (scaling,
normalization, probe masks, baseline experiment, values for usermodifiable Statistical Expression algorithm parameters). For more
information about usersets, see Userset Tab, on page 415.
In a batch analysis, the settings for the default userset are specified
in the Expression Analysis Settings dialog. The default userset is
not the userset specified during experiment setup.
1.
To select other than the default userset, double-click the Userset
column.
This displays a drop-down list of available usersets (Figure 11.7).
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303
If a userset with a baseline experiment is selected and the field
under the baseline column is empty, the baseline experiment from
the userset is used during the analysis.
Figure 11.7
Batch Analysis window, drop-down list of usersets
2.
Select a userset from the drop-down list; or
Highlight the cell intensity data of interest, select Edit → Select
Userset from the menu bar, then make a selection from the dropdown list.
SELECTING A BASELINE FOR A COMPARISON EXPRESSION ANALYSIS
1.
In the Batch Analysis window, double-click in the baseline
column of the cell intensity data for the comparison expression
analysis (Figure 11.8); or
Select the .cel of interest and choose Edit → Select Baseline from
the menu bar.
The Select Baseline Data dialog box appears (Figure 11.9).
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Figure 11.8
Batch Analysis window
Figure 11.9
Select Baseline dialog box, List view (left) and Details view (right)
Click Details
to display experiment and sample information
for the data.
3. To filter the data in the Select Baseline dialog box:
2.
Click Filter.
This displays the advanced filter (Figure 11.10).
B. Make selections from the drop-down lists.
A.
C.
Click Apply.
chapter 11 | Batch Analysis
Figure 11.10
Select Baseline dialog box, advanced filter
4.
Double-click the baseline data.
The Batch Analysis window displays the baseline data
(Figure 11.11).
Figure 11.11
Batch Analysis window, baseline selected
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Affymetrix® GeneChip® Operating Software User’s Guide
To clear a baseline from the batch analysis window, right-click the
baseline data and select Clear Baseline from the shortcut menu
that appears; or
Click the baseline experiment and select Edit → Clear Baseline
from the menu bar.
Renaming Results from Batch Analysis
To reanalyze experiments without overwriting existing analysis
output, rename the output .chp data from the batch analysis using one
of the following methods:
• Renaming Results Automatically (see below)
• Renaming Results Individually (see page 307)
RENAMING RESULTS AUTOMATICALLY
If you select .cel data for batch analysis, GCOS can automatically
rename all of the output .chp data by adding a user-specified prefix
and/or suffix to the data name.
If you select .chp data for batch analysis, the prefix or suffix are not
applied to the output name.
1.
Click the Options button or select View → Options from the
menu bar.
The Batch Analysis Options dialog box appears (Figure 11.12).
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307
Figure 11.12
Output Naming Options dialog box
2.
To add a prefix to the .chp name, choose the Prefix option and
enter a prefix for the name in the associated box.
To add a suffix to the .chp name, choose the Suffix option and
enter a suffix for the name in the associated box.
4. Click OK.
When cell intensity data are placed in the Batch Analysis window,
the user-specified prefix and/or suffix is automatically added to the
output analysis name.
3.
RENAMING RESULTS INDIVIDUALLY
You can individually rename an output results from the batch analysis.
Editing the Output Name
To edit the default name, do either of the following:
• Double-click the name in the Batch Analysis window and enter a
new name.
• Select the cell intensity data of interest in the Batch Analysis
window, select Edit → Rename Output Data from the menu
bar, and enter a new name.
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Adding a Prefix or Suffix to the Output Name
1.
In the Batch Analysis window, use one of the following methods
to select one or more outputs.
- To select all data, right-click a name and click Select All in
the shortcut menu that appears; or
Select View → Select All from the menu bar.
- To select adjacent data, press and hold the Shift key while you
click the first and last name in the selection.
- To select non-adjacent data, press and hold the Ctrl key while
you click the names.
2.
Right-click the selected outputs and select Set Prefix/Suffix from
the shortcut menu that appears; or
Click the selection and select Edit → Set Prefix/Suffix from the
menu bar.
The Set Prefix/Suffix dialog box appears (Figure 11.13).
Figure 11.13
Set Prefix/Suffix dialog box
3.
Enter a prefix and/or suffix, then click OK.
The prefix and/or suffix are added to the selected output names.
Removing Data from the Batch Analysis Window
To remove cell intensity data from the Batch Analysis window, do
either of the following:
• Select the data name and click the Remove button
.
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309
• Select the data name, then select Edit → Remove Item from the
menu bar.
Running a Batch Analysis
To run the batch analysis, click the Analyze button ; or
Select Edit → Start Analysis from the menu bar.
2. To stop a batch analysis in progress, click the Stop button
Select Edit → Stop Analysis from the menu bar.
The software completes the current analysis and cancels the
remaining data in the batch analysis queue.
1.
; or
RESUMING A BATCH ANALYSIS
If the batch analysis is interrupted before all analyses are completed,
GCOS can resume the run and analyze the remaining .cel data in the
batch.
To resume a batch analysis:
Open the Batch Analysis window.
The Batch Analysis window displays the remaining unanalyzed
data.
2. Click the Analyze button
; or
Select Edit → Start Analysis from the menu bar.
1.
Exporting a Batch File
The Batch Analysis window contents can be exported to a text file (tab
delimited .txt). The batch file provides a record of the analysis and can
be imported for a subsequent batch analysis.
1.
Select Edit → Export Batch from the menu bar.
The Export Batch dialog box appears (Figure 11.14).
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Figure 11.14
Export Batch dialog box
2.
Enter a name for the batch file, then click Save.
The batch file (.txt) is created (Figure 11.15).
Figure 11.15
Batch file (.txt)
Importing a Batch File
GCOS can import a batch file (tab delimited .txt) that follows the
format shown in Figure 11.15.
To import a batch file:
1.
Open the Batch Analysis window.
2.
Select Edit → Import Batch from the menu bar.
The Import Batch dialog box appears (Figure 11.16).
chapter 11 | Batch Analysis
Figure 11.16
Import Batch dialog box
3.
Double-click the batch file (.txt) you want to import.
The batch file is imported to the Batch Analysis window.
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Chapter
12
Publishing Data
Chapter
12
315
Publishing Data
GCOS can copy expression sample and experiment data, including cell
intensity data and probe analysis data from the process database to a
publish database. This is called publishing. Published expression data
can be queried by the Affymetrix® Data Mining Tool (DMT) software
or several other third party analysis tools.
Register sample & define experiment
Process probe array in fluidics station
Scan probe array & save image data
Compute cell intensity data from
image data & save cell intensity data
Analyze expression cell intensity data
& save expression probe analysis data
Publish expression data
Generate an expression report
Figure 12.1
Assay & analysis flow chart
This chapter includes the following sections:
• Selecting the Publish Database (see below)
• Specifying the Task (see page 316)
• Publishing Options (see page 320)
• Publishing, Canceling, or Restarting a Task (see page 321)
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Selecting the Publish Database
1.
In the GeneChip Software shortcut bar, click Publish
; or
Select Run → Publish from the menu bar.
This displays the publish window (Figure 12.2).
The top windowpane displays all publish databases. The bottom
windowpane displays a status log of tasks.
Figure 12.2
Publish window
2.
Click the publish database destination for the data.
A yellow icon indicates the currently selected database. A gray icon
indicates an unselected database.
Each database requires a login password before publishing can
proceed.
Specifying the Task
A task consists of all data selected for publishing. Each experiment or
type of data to be published is called a task item. Table 12.1 shows the
data that are published for each type of task item.
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317
Table 12.1
Data published for different types of task items
Task Item
Data Published
Experiment
All cell intensity data associated with the
experiment.
All probe analysis data associated with
the experiment.
Image data
All cell intensity data associated with the
experiment.
All probe analysis data associated with
the experiment.
Cell intensity data
The associated experiment.
The cell intensity data.
All probe analysis data associated with
the cell intensity data.
Probe analysis data
The associated experiment.
The probe analysis data.
All cell intensity data associated with the
probe analysis data.
To select the tasks, use either of the following methods:
Using the Drag-and-Drop Method
Drag the task item that you want to publish from the data tree
onto a database icon in the top pane of the publish window.
2. Repeat the drag-and-drop operation for the remaining task items
to be published (Figure 12.5).
1.
Using the Add Toolbar Button
1.
Click the Add button or select Publish → Add Item from the
menu bar.
The Open dialog box appears (Figure 12.3).
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Figure 12.3
Open dialog box, list view (left) and details view (right)
2.
Click Details to display experiment and sample information for
each data type.
3.
To filter the list of data types in the Open dialog box, click Filter
The advanced filters are displayed (Figure 12.4).
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319
Figure 12.4
Open dialog box, advanced filter
Make selections from the drop-down lists and click Apply to filter
the list.
5. Make a selection from the Data Type drop-down list and select the
data to be published.
To select adjacent data, press and hold the Shift key while you
click the first and last name in the selection. To select non-adjacent
data, press and hold the Ctrl key while you click the names.
6. Click OK to add the data to the selected publish database
(Figure 12.5).
7. To remove a task item from the publish window, select the task
item in the publish window and click the Remove button ;or
Choose Publish → Remove Item from the menu bar.
4.
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Figure 12.5
Publish window
Publishing Options
You may publish intensity data or overwrite a previously published
task item. You must be authorized by the GCOS administrator to
overwrite data. The status bar at the bottom of the publish window
displays the publishing options (Figure 12.5).
You can select from the following options:
• Publishing Intensity Data (see below)
• Overwriting Data (see page 321)
PUBLISHING INTENSITY DATA
Cell intensity data (.cel) are not automatically published. Publishing
.cel data uses large amounts of computer memory. For example,
publishing the probe analysis data for a high density probe array
requires approximately 2 MB of disk space compared to 30 MB for
both the probe analysis and cell intensity data.
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321
The image data are not published.
To include cell intensity data in the publish database, select
Publish → Options → Publish Intensities from the menu bar.
The Publish Intensities menu item is check marked.
2. To not include cell intensity data in the publish database, select
Publish → Options → Publish Intensities from the menu bar to
remove the check mark.
1.
OVERWRITING DATA
A previously published task item can be overwritten. Users must be
authorized by the GCOS administrator to overwrite data.
• Select Publish → Options → Overwrite Data from the menu
bar.
Publishing, Canceling, or Restarting a Task
You can use the Publish window for:
• Publishing the Task (see below)
• Canceling a Task (see page 322)
• Restarting a Publishing Task (see page 322)
It is recommended that users not publish and restore to the same
publish database simultaneously. Sometimes the restore will be
rejected and sometimes the publishing will be rejected. If the
restore of a publish database fails, an error message is displayed.
PUBLISHING THE TASK
1.
After you have specified the task, click the Publish button
; or
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Select Publish → Publish from the menu bar.
The Publish Login dialog box appears if this is the first time
during the session that an item has been published to the database
(Figure 12.6).
Figure 12.6
Publish Database Login
2.
Enter the password for the database.
The task is displayed in the task log and will be published during
the time frame specified by the GCOS administrator.
CANCELING A TASK
You can cancel tasks waiting to be published (the status in the task log
is WAIT).
Select the task in the task log.
2. Click the Cancel button
; or
Select Publish → Monitor → Cancel Publish from the menu bar.
The task is now canceled (the status is CANCELED).
1.
RESTARTING A PUBLISHING TASK
You can reinstate or restart a canceled task and return it to the
publishing queue.
1.
Select the canceled task in the task log.
2.
Click the Restart button ; or
Select Publish → Monitor → Restart Publish from the menu
bar.
chapter 12 | Publishing Data
The task is now restarted (the status is WAIT) and will be
published during the time frame specified by the GCOS
administrator.
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Chapter
13
Defaults
Chapter
13
327
Defaults
This chapter explains how to change the factory set defaults for:
• image settings
• data locations
• fluidics station configuration
• analysis prompts
• experiment data storage
This chapter contains the following sections:
• Viewing Default Settings (see below)
• Fluidics Settings (see page 333)
• Scanner Settings (see page 334)
• Analysis Settings (see page 335)
The following Defaults settings are described in Chapter 5, Getting
Started, on page 53:
• Cell Intensity Analysis Options (see page 598)
• Cell Intensity Analysis Options (see page 598)
• Setting Archiving Options for DAT files (see page 599)
Viewing Default Settings
• Select Tools → Defaults from the menu bar.
The Defaults dialog box appears (Figure 13.1).
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Figure 13.1
Defaults dialog box, Image Settings tab
IMAGE SETTINGS
The image settings (Figure 13.1) affect the display of image and cell
intensity data in the Image window. For more information on this
window, see Introduction, on page 141.
The image settings specified in the Defaults dialog box (except for
the color option) are applied to subsequently opened image or cell
intensity data and do not affect active, open data.
Intensity Range
GCOS software records a dynamic intensity range from 0 to 65,000
and provides 256 colors from black through white for image display.
The intensity range of an image is divided into 256 bins and each bin
is assigned a color or gray scale.
You may enter a new lower or upper limit for the intensity range
associated with an image and apply this subset of the dynamic range
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329
to the image. Lowering the upper limit increases the image brightness
and raising the lower limit decreases the brightness.
Using this image scaling process, you can adjust the display of a data or
cell intensity file for optimum viewing. Alternatively, GCOS can
automatically scale the image using the minimum and maximum
pixel intensities of the image.
To automatically scale an image, choose the Autoscale option in
the Defaults dialog box (Figure 13.1) and click OK.
2. In the Image Settings dialog box for the current image or cell
intensity data, you may click Defaults to return the intensity
parameters (Autoscale option and Intensity range) to the settings
in the Image Settings tab of the Defaults dialog box. For more
information about the Image Settings dialog box, see Making
Adjustments to the Current Image or Cell Intensity Data Only, on
page 197.
1.
Color
You can view the pixel intensity values in gray scale or pseudo color
(generated by applying rainbow colors to the intensity scale). Choose
the Color Bar option (Figure 13.1) to display a gray scale or pseudo
color bar at the top of the Image window.
Coordinates
When you click the image, a red cross hairs marks the location. The
status bar at the lower left of the main window displays the intensity
data and x-y coordinates of a probe cell or pixel indicated by the cross
hairs.
If you choose the Cell option in the Defaults dialog box (Figure 13.1),
a pop-up tool tip and the status bar display the x-y coordinates of the
cell, the cell intensity, and the pixel intensity (Figure 13.2).
If you choose the Pixel option, the pop-up tool tip and the status bar
display the x-y coordinates of the pixel and the pixel intensity
(Figure 13.2).
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Cell X = 186, Y = 41, Cell Intensity = 22561.8, Pixel Intensity =
Figure 13.2
Image data, probe cell coordinates (top) and pixel coordinates (bottom)
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331
Pixel X = 1727, Y = 573, Intensity = 22409
Figure 13.2
Image data, probe cell coordinates (top) and pixel coordinates (bottom)
Highlight Colors
You may specify new highlighting colors for the grid, masked cells,
outlier cells, or highlighted probe array cells (features).
1.
Click Highlights in the Defaults dialog box (Figure 13.1).
The Highlight Colors dialog box appears (Figure 13.3).
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Figure 13.3
Highlight Colors dialog box
2.
To change the color of a particular item (for example, the grid
overlay):
Click the associated color box in the Highlight Colors dialog
box.
The Color palette is displayed (Figure 13.4).
A.
Custom color
Figure 13.4
Color palette
Luminosity
scale
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333
To select a predefined color, click one of the basic colors.
C. To define a custom color, click Define Custom Colors, then
use the click-and-drag method to move the cross hairs in the
custom color field. Adjust the color brightness using the
luminosity scale to the right. When finished, click Add to
Custom Colors to apply the color.
The new color is applied to the selected item.
B.
D.
Click OK to close the Color palette.
Grid Overlay
Choose the Grid Overlay option (Figure 13.1) to automatically
display the grid on a image or cell intensity data. Remove the check
mark to toggle the grid overlay off. Alternatively, click Grid in the
Image window task bar (or press the G key) to toggle the grid on or off.
Fluidics Settings
In the Fluidics tab (Figure 13.5) you can:
• Specify the number of fluidics stations installed on the system (up
to eight fluidics stations may be simultaneously controlled by one
work station).
• Specify each fluidics station’s number and ID.
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Figure 13.5
Defaults, Fluidics tab
Notification Message when
protocol is complete
Choose this option to display a notification of
completion at the end of a protocol
Scanner Settings
In the Fluidics tab (Figure 13.6) you can:
• specify whether a scanner is installed on the system
• if a scanner is installed, choose the option to turn on the laser at
startup
If the AutoLoader is installed, you can:
• choose to use it in manual mode
• choose to disable it.
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335
Figure 13.6
Defaults, Scanner tab
Scanner Installed
Choose this option after the scanner is installed.
Turn on Laser at startup
Confirm this option is chosen (default) so that the laser
automatically turns on when GCOS is started.
Enable Manual Mode
Choose this option if you are using a scanner equipped
with the AutoLoader and would like to disable the
AutoLoader’s autorun feature. This will allow you to
add and scan cartridges one at a time.
Disable AutoLoader
Choose this option if you are using a scanner equipped
with the AutoLoader and would like to disable the
AutoLoader completely. This will allow you to use the
software without communicating with the AutoLoader.
Analysis Settings
The Analysis Settings tab (Figure 13.7) displays two options that are
available when a batch analysis is run.
The other settings of the Analysis Settings tab are described in Cell
Intensity Analysis Options, on page 598.
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Figure 13.7
Defaults, Analysis Settings tab
PROMPT FOR OUTPUT DATA NAME
1.
Choose the Prompt for output data name option (Figure 13.7)
to display a Save Results As dialog box (Figure 13.8) at the start of
an analysis.
The default name for the probe analysis data is the same as the
experiment name. The Save Results As dialog box displays the
default name.
Figure 13.8
Save Results As dialog box
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2.
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Click OK to keep the default data name; or
Enter a new name and click OK.
DISPLAY SETTINGS WHEN ANALYZING DATA
Choose the Display settings when analyzing data option
(Figure 13.7) to display the Expression Analysis Settings dialog box
(Figure 13.9) at the start of an analysis.
Figure 13.9
Expression Analysis Settings dialog box
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Chapter
14
Printing
Chapter
14
341
Printing
This chapter explains how to print:
• image data
• cell intensity data
• probe analysis data
• reports
It contains the following sections:
• Printing Image or Cell Intensity Data (see below)
• Printing Probe Analysis Data (see page 342)
• Printing an Expression Report (see page 343)
Printing Image or Cell Intensity Data
1.
When the Image window is open, click the Print button
select File → Print from the menu bar.
The Print dialog box appears (Figure 14.1).
No print range options are available.
Figure 14.1
Print dialog box in the Image window
or
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Click OK to print the image or cell intensity data.
Printing Probe Analysis Data
You may print tabular data and graphs from the Expression Analysis
window (EAW).
1.
When the EAW is open, click the Print button
→ Print from the menu bar.
The Print dialog box appears (Figure 14.2).
or select File
Figure 14.2
Print dialog box, EAW
The All and Selection options apply only to the Experiment
Information, Metrics, and Pivot tables. If the Graphics option is
chosen, the displayed graphs are automatically printed.
2. Choose Results and:
- All to print the entire table in a tab (Experiment Information,
Metrics, or Pivot).
- Selection to print only highlighted table rows.
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Printing an Expression Report
You may print all or selected pages from an expression report.
1.
When a report is open in the main display area, click the Print
button
or select File → Print from the menu bar.
The Print dialog box appears (Figure 14.3).
Figure 14.3
Print dialog box, report (.rpt)
2.
Choose:
- All to print all pages of a report.
- Pages and enter a page range to print selected pages of a
report.
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Chapter
15
GCOS Manager
Chapter
15
347
GCOS Manager
The GCOS Manager application provides software tools to:
• Manage the GeneChip® data in the process and publish databases.
• Define and manage templates for sample registration and
experiment setup.
• Create usersets for analysis.
• Create and manage publish databases.
• Import data to the process database.
• Export experiment and analysis data.
• Archive and restore analysis data.
• Create and manage roles that define user access privileges
(available only to users connected to a GCOS server).
This chapter explains the GCOS Manager functions and how to use
them. It contains the following sections:
• Getting Started (see below)
• Process Tab (see page 356)
• Publish Tab (see page 381)
• Import Tab (see page 396)
• Userset Tab (see page 415)
• Template Tab (see page 425)
• Roles Tab (see page 441)
Getting Started
To start the GCOS Manager:
• Click the Microsoft® Windows® Start menu button
, then
select Programs → Affymetrix → GCOS Manager.
The GCOS Manager starts and displays the user interface
(Figure 15.1).
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The software functions are organized in the following tabs:
- Process (see page 356)
- Publish (see page 381)
- Import (see page 396)
- Userset (see page 415)
- Template (see page 425)
- Roles (see page 441)
The Roles tab is available when the GCOS Manager is connected to
a GCOS server.
Table 15.1 lists the functions found in each tab.
To select the active server:
• Make a selection from the server drop-down list in the toolbar
(Figure 15.1 and Figure 15.2).
chapter 15 | GCOS Manager
Menu
bar
Server drop-down list
Toolbar
Active
server
Tabs
Active
server
Process
database
Figure 15.1
GCOS Manager user interface, Microsoft® MSDE workstation database
Roles tab is only
available to users
connected to a
GCOS server
Figure 15.2
GCOS Manager user interface, GCOS server database
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Table 15.1
GCOS Manager tab functions for Affymetrix® GeneChip® data
GCOS Manager
Tab
Functions in This Tab
Process
Archive or restore experiment data (.dat, .cel, .chp).
Delete process data.
Export experiment data.
Assume ownership of data (available only to users
connected to a GCOS server).
Print an experiment.
Register or unregister the local workstation or GCOS server.
Publish
Delete published data or a probe array type from a publish
database.
Create a publish database.
Import
Import experiment data to the process database
Userset tab
Create or modify a userset (a set of predefined parameter
settings for the Statistical Expression algorithm).
Delete a probe array type from a userset.
Delete a userset.
Template
Create a template (a predefined form used to register
samples and define experiments in GCOS 1.4).
Deactivate or activate a template for use in GCOS 1.4.
Rename a template.
Roles
(available only
to users
connected to a
GCOS server)
Create a role (a defined set of user privileges).
Delete a role.
You can learn more about GCOS in the following sections:
• GCOS Manager Icons (see below)
• Terminology (see page 352)
GCOS MANAGER ICONS
Table 15.2 shows the icons used in GCOS Manager.
chapter 15 | GCOS Manager
Table 15.2
GCOS Manager Icons
Sample
Template
Properties information
Project
Global
Gray bullet indicates
processes that have been
completed.
Experiment information
Server
Green bullet indicates
processes waiting to
commence.
Scanned probe array
image data (.dat)
Process database
(yellow)
Computed cell
intensities (.cel)
Publish database
(gray)
Export status
Probe analysis data
(.chp)
Import to database
Import status
Probe array type
Domain
Delete status
Chip
User group
Archive status
Vessel
User
Create publish database
status
Userset
Role
Filter
Red check mark on an
experiment, .dat, .cel, or
.chp icon(s) indicates that
the data already exist in the
publish database.
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TERMINOLOGY
Table 15.3 lists terms that are used frequently throughout this
chapter. For your convenience, the terms are listed under the tabs
where they are most frequently found.
Table 15.3
Terminology common to all tabs
Data & Object
Types Across All
Tabs
Definition
Automate
A monitored task whose status, either on or off, is
viewed in the Local Task pane. Automate On
indicates GCOS will automatically track an experiment
through data analysis after the probe array has been
scanned.
Sample
A set of experiments.
Experiment
Specifies the type of probe array to which the target
(sample) will be hybridized as well as other information
relevant to the experiment. The experiment name
provides the name for the data types that are
subsequently generated in the analysis.
Note: The Import tab shows experiment, cell intensity,
or probe analysis data that can be imported or copied to
the process database. In GCOS, the process database
includes the experiment and sample data.
Image data (.dat)
The .dat file contains the image data of the scanned
probe array data acquired in GCOS. The image data
along with the image attributes stored in the database
define the raw image data.
Cell intensity data
(.cel)
The cell file (.cel) of computed intensities that GCOS
automatically generates from the image data file (.dat).
GCOS can publish the .cel to a publish database where
it is accessible to the Affymetrix® Data Mining Tool
(DMT).
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Table 15.3
Terminology common to all tabs
Data & Object
Types Across All
Tabs
Definition
Probe analysis data
(.chp)
The probe analysis output or chip file that is generated
by the GeneChip data algorithms. GCOS can publish
expression .chp to a publish database where it is
accessible to the Affymetrix® DMT.
Table 15.4
Terminology in the Process tab
Process Tab Terms
Definition
Active server
More than one GCOS server may be registered. The
active server refers to the GCOS server where the
displayed process database resides.
Archive
Move files from the process database to an external
location.
Unarchive
Restore archived files to the process database.
Export
Copy data from the process database and send to an
external location.
Note: For an export from GCOS to Microarray Suite
(MAS) 5.x, data created in GCOS are used to generate
data files that are added to the default file location in
MAS.
Process database
Database residing on the workstation or GCOS server
that contains experiment and sample data. There is
only one process database per workstation or GCOS
server.
Project
A set of experiments with a common bond that are
grouped together by their affiliation with a project. A
project is created during sample registration in GCOS.
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Table 15.5
Terminology in the Publish tab
Publish Tab Terms
Definition
Affymetrix® Analysis
Data Model (AADM)
The AADM is the relational database schema that
Affymetrix uses to store experiment data (.dat, .cel, .chp) in
the publish database so that results may accessed by the
Affymetrix® Data Mining Tool and other third party
analysis tools. The AADM includes additional tables to
support expression results. The AADM is publicly available
to support open access to experiment information
generated and managed by Affymetrix® software.
Cell intensities
The computed intensities that GCOS automatically
generates from the image data (.dat). GCOS can copy or
publish the cell intensity data to a publish database.
Publish database
An AADM database residing on a server that contains
select published process data. More than one publish
database may reside on a single server.
Publish
To copy or migrate experiment data to an AADM database
on the workstation or GCOS server.
Table 15.6
Terminology in the Import tab
Import Tab Terms
Definition
Create Sample
Creating a sample captures sample information and
identifies the relationship between the experiment and
experiment data (.cel, .chp) that are being imported.
Import
Copies experiment data (.cel, .chp) created in GCOS to the
process database on the workstation or the GCOS server.
Note: For an import to GCOS from Microarray Suite (MAS)
5.X, data are extracted from the experiment data files
created in MAS and are added to the process data base.
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Table 15.7
Terminology in the Userset tab
Userset Tab Terms
Definition
Userset
A predefined set of values for modifiable parameters in the
Statistical Expression algorithm.
Independent
parameter
Static settings defined in the userset that are not influenced
by the probe array type.
Dependent
parameters
Settings defined in the userset that are specific to a
particular probe array type.
Table 15.8
Terminology in the Template tab
Template Tab
Terms
Definition
Activate
Restores an inactive (deactivated) attribute or template.
Template
A form created by the administrator that defines the
attributes and values which are required to register
samples and define experiments in GCOS.
Deactivate attribute
Renders an attribute inactive. The attribute is not
permanently removed from the system. A deactivated
attribute does not appear in GCOS until it is restored by the
Activate command.
Deactivate template
Permanently deletes a template from the system if it is not
currently used by an experiment or sample. Otherwise, the
template is deactivated and does not appear in GCOS until
it is restored by the Activate command.
Table 15.9
Terminology in the Roles tab
Roles Tab Terms
Definition
Privileges
The functions or permissions that define a role.
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Table 15.9
Terminology in the Roles tab
Roles Tab Terms
Definition
Role Definitions
Identifies the first branch under the active server where the
role names are listed.
Role
A defined set of user access privileges.
User Definitions
Identifies the branch under the process database where
role membership is defined.
Process Tab
This section of the manual explains the layout of the Process Tab
window, its functions, and how to accomplish tasks here.
The Process tab shows you the data in the system for all registered
servers, where the data are found, and environmental property
information about the data.
The Process tab window is divided into three windowpanes
(Figure 15.3).
You can learn more about the Process Tab in the following sections:
• Process Tab Windowpanes (see page 357)
• Process Tab Functions (see page 358)
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Active
server
Process
database
tree
Selected data
Task status/
Properties
Figure 15.3
Process tab windowpanes
PROCESS TAB WINDOWPANES
The Process Tab window (Figure 15.3) has the following panes:
Process
database
tree
Shows the active server, process database, and data types (samples,
projects, and types of probe arrays). The data type subfolders contain
samples
, projects
, or probe array types
. Click a sample or
project to display the associated experiment data (.dat, .cel, .chp) in the
data pane.
Selected
data
Shows the experiment data of the sample or project selected in the process
database tree. The first time you click an experiment
in the tree of
selected data, the information is read and a + sign appears next to the
experiment name. Click the + sign to display the associated data.
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Task
Displays the property information or local task view, depending on the
status/
item selected in process database tree or the selected data pane. Property
Properties information is defined by the template that was used during sample
registration in GCOS. The task status view shows the status of processes
that may be occurring in the database (for example, export, import, delete,
archive, or create). In the task status view, you can monitor these jobs
while you work on other tasks in the system.
PROCESS TAB FUNCTIONS
The primary tasks in the Process tab are:
• Archive data (see page 359)
• Unarchive data (see page 361)
• Change ownership of data (see page 362)
• Delete process data (see page 364)
• Deleting a probe array type (see page 366)
• Export data (see page 368)
You can also use the tools in the Process tab to:
• Register a GCOS server (see page 369)
• Unregister a GCOS server (see page 371)
• View Server Events (see page 371)
• View and manage Publish tasks (see page 372)
• Search the Process database (see page 376)
• Filter samples displayed in the data tree (see page 380)
The primary data types in the Process tab are:
• sample
• project
• experiment
• image data, cell intensity data, and probe analysis data
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The tasks associated with each data type are found under Process in
the menu bar. Alternatively, right-click an item to view a shortcut
menu (Figure 15.4).
Sample
shortcut
menu
Probe
array
type
shortcut
menu
Project
shortcut
menu
File
shortcut
menu
Figure 15.4
Process tab shortcut menus
Archiving Data
Archiving data moves a user-selected data type to an external storage
location. An archived data type no longer exists in the process
database; however, its representative icon remains in the data tree and
appears gray to indicate the data are available through the unarchive
process.
1.
In the Process tab, click the sample or project that contains the
data you want to archive.
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In the data pane, right-click the data that you want to archive and
select Archive from the shortcut menu that appears (Figure 15.4);
or
Click the data and select Process → Archive Data Path from the
menu bar.
The Select Archive Data Path dialog box appears (Figure 15.5).
Figure 15.5
Select Archive Data Path dialog box
Select a drive from the Drive drop-down list and navigate to the
directory where you want to archive the data.
4. Click OK.
The data are archived in the specified directory.
3.
To view more information about the archive task status, right-click
in the Task Status/Properties pane and select View Task Log
from the shortcut menu that appears (Figure 15.6); or
Double-click
to view the archive task log (Figure 15.7).
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Figure 15.6
Task Status/Properties pane
Figure 15.7
Archive task log
Use the Find function to generate a list of files associated with a
specific project. Next, SHIFT-select and archive the data in one quick
step. This is only available for .dat, .cel, and .chp files in the process
database.
Unarchiving Data
The icon for archived data appears gray. The unarchive command
restores archived data to the process database.
1.
In the Process tab, click the sample or project that contains the file
you want to unarchive.
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In the data pane, right-click the data that you want to unarchive
and select Unarchive from the shortcut menu that appears
(Figure 15.4 on page 359); or
Click the data and select Process → Unarchive from the menu
bar.
Selecting the parent data includes all related child data in the
unarchive process.
If GCOS Manager cannot find the archived file, a Data Location
dialog box appears. Enter the location of the data you want to
unarchive in this dialog box.
The data are unarchived and restored to the process database on the
active server.
The Process window does not automatically refresh upon
completion of the Archive or Unarchive task. Therefore, if you
unarchive data, the icon remains gray even though the task was
completed successfully. To refresh the view, select View → Refresh
from the menu bar.
Changing Data Ownership
If needed for security or management purposes, you can assume or
assign ownership of data (change the user attribute of data).
This feature is only available to users connected to a GCOS server.
If the Take Ownership Process Data option is defined for a user in
the Roles tab, the user can:
• assume ownership of samples, experiments, or analyses.
• assign ownership of samples, experiments, or analyses to a user
who is also a member of a user group that the assignor belongs to.
(For more information on role definition, see Roles Tab, on page 441).
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Data ownership means you have permission to overwrite a file with
new contents. For example, an owner can reanalyze cell intensity data
using different parameter settings for the Statistical Expression
algorithm to generate new probe analysis data.
Assuming Ownership
In the Process tab, right-click the sample, project, or data of
interest.
2. Select Assume Ownership from the shortcut menu that appears.
Your user name is displayed in the Task Status/Properties pane
(Figure 15.9).
1.
Assigning Ownership
1.
In the Process tab, right-click the sample, project, or data of
interest.
2.
Select Assign Ownership from the shortcut menu that appears.
The Assign Owner dialog box appears (Figure 15.8).
Figure 15.8
Assign Owner dialog box
3.
Enter the name of the new owner, and click OK.
The user name of the new owner is displayed in the Task Status/
Properties pane (Figure 15.9).
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Data
owner
Task status/
Properties
Figure 15.9
Process tab, Task status/Properties pane shows the user name of the owner of the selected data
Deleting Process Data
You can delete samples, experiments, experiment data (.cel, .chp), or
usersets. Deleting a sample deletes all associated experiments and
analyses (.cel, .chp). Deleting an experiment deletes the associated
analyses (.cel, .chp).
The Delete option permanently removes data from the database.
There is no restore function to recover deleted data.
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1.
365
Right-click the item that you want to delete, and select Delete
from the shortcut menu that appears; or
Click the item and select Process → Delete from the menu bar.
A warning/confirmation box appears (Figure 15.10).
Figure 15.10
Delete warning/confirmation box
2.
Click Yes to continue.
The Task Status/Properties pane displays the delete local task
status.
To view more information about the delete task status, right-click
in the Task Status/Properties pane and select View Task Log
from the shortcut menu that appears (Figure 15.11); or
Double-click
to view the delete task log (Figure 15.12).
Figure 15.11
Task Status/Properties pane
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Figure 15.12
Delete task log
Deleting process data is different from deleting publish data (see
Chapter 12, Publishing Data, on page 315). Deleting published data
removes only the data that has been published to a publish
database. The data source in the process database remains
available.
Deleting a Probe Array Type
You can remove an unused or unwanted probe array type from the
process database.
Deleting a probe array type deletes the associated usersets. The
data created with these usersets remain, but are not accessible.
1.
In the process pane data tree, expand the assay folder (for example,
Expression) under the Probe Array Type folder (Figure 15.13).
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Figure 15.13
Process pane
2.
Right-click the probe array type that you want to delete and select
Delete from the shortcut menu that appears; or
Click the probe array type and select Process → Delete from the
menu bar.
A warning/confirmation box appears (Figure 15.14).
Figure 15.14
Delete warning/confirmation box
3.
Click Yes to continue.
The selected probe array type is removed from the process
database.
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Exporting Data
You can export (copy) sample or experiment data (.dat, .cel, .chp) to
an external storage location.
Sample and experiment information are exported to an Affymetrix®
Microarray Suite 5.x .exp file.
1.
In the Data pane, right-click the item that you want to export and
select Export from the shortcut menu that appears; or
Select the item and click the Data Path button
or select Tools
→ Data Path from the menu bar.
Selecting an object includes all of the data that are associated with
it. For example, selecting image data (.dat) includes any related
cell intensity data (.cel) and probe analysis data (.chp).
The Select Export Data Path dialog box appears (Figure 15.15).
Figure 15.15
Select Export Data Path dialog box
2.
Choose a drive from the Drive drop-down list and a directory path
from the Directories box.
Click Network to map a network drive to a drive letter.
4. Click OK.
3.
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The Task Status/Properties pane displays the export local task
status.
To view more information about the export task status, right-click
in the Task Status/Properties pane and select View Task Log
from the shortcut menu that appears (Figure 15.16); or
Double-click
to view the export task log (Figure 15.17).
Figure 15.16
Task Status/Properties pane
Figure 15.17
Export task log
Registering a GCOS Server
Registering a GCOS server makes it available to GCOS Manager.
1.
Click the
button or select Tools → Register GCOS Server
from the menu bar.
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The Register GCOS Server dialog box appears (Figure 15.18).
Figure 15.18
Register GCOS Server dialog box
2.
Select the server that you want to register and click OK.
The selected server is added to the drop-down list on the toolbar
and becomes the active server.
If the selected server is not GCOS aware, an error message is
displayed (Figure 15.19).
Figure 15.19
Register GCOS Server error message
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The error message indicates that there is no GCOS Server software
installed, or that there is an installation error. For further
information, please refer to the Affymetrix® GeneChip® Operating
Software Server Installation and Administration Guide.
Unregistering a GCOS Server
• In the process pane, right-click the GCOS server that you want to
remove and select Unregister GCOS Server from the shortcut
menu that appears.
Viewing Server Events
The server events option displays a log of the events that occurred on
the active server.
• To display the Event Viewer, click the Server Events button
or select Tools → Server Events from the menu bar
(Figure 15.20).
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Figure 15.20
Event Viewer shows an event log for the active server
Viewing the Publish Tasks
You can use the Server Task option to view the publishing queue on
the active server.
Click the Server Tasks button or select Tools → Server Tasks
from the menu bar.
The task list for the active server appears and shows all items in the
publishing queue (Figure 15.21).
2. To sort the task list in ascending order, click a column header to
define the primary sort order (for example, the Started column
header). To sort the task list in descending order, click the same
column header again.
1.
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Click to view the task list menu or
right-click a task in the list.
373
Select a column header to define the primary sort order.
Click the header once to sort the task list in ascending
order. Click again to sort in descending order.
Service status
Figure 15.21
Task list displays the publishing queue on the active server
Task List Items & Commands
indicates a new task in the queue waiting to be published
blue check mark indicates a task that is being published
green check mark indicates a completed (published) task
indicates an incomplete task that was not published due to an error
To view the task list commands, click the icon (upper left corner of
the window) (Figure 15.21) or right-click a task to display a shortcut
menu.
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Table 15.10
Task list menu commands
Command
Use this command to...
View Tasks
Display the status of each task in the publishing queue on
the active server (Figure 15.22).
View Task Items
Display all items for a selected task (Figure 15.22).
View All Items
Display all items for all tasks in the Task List window.
Cancel
Cancel a pending publish task.
Restart
Reactivate the publish process for a cancelled task.
Save As
Save the task list to a text file (.txt).
Delete Task Items
Remove all task items from the Task List window.
Figure 15.22
Server Task window, View Task Items command displays all items for a selected
task
Saving the Task List
You can save the items in the Server Task window to a text file (.txt).
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1.
375
Right-click a task in the Server Task window and select Save As
from the shortcut menu that appears: or
Click the
icon in the upper left corner of the Task List window
and select Save As from the drop-down menu.
The Save As dialog box appears (Figure 15.23).
Figure 15.23
Save As dialog box
From the Save in drop-down list, navigate to the destination
where you want to save the .txt file.
3. Name the file and click Save.
The task list is saved as a text file in the defined destination.
2.
Deleting Task Items
To remove all of the task items from the Server Task Window:
1.
Right-click a task and select Delete Task Items from the shortcut
menu that appears; or
Click the
icon in the upper left corner of the Task List window
and select Delete Task Items from the drop-down menu.
A warning/confirmation window appears (Figure 15.24).
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Figure 15.24
Task Delete warning/confirmation
2.
Click Yes to delete all tasks on and before the date and time
indicated.
The items are deleted and Server Task window is empty.
Cancelling or Restarting an Active Publish Task
• To stop the publish process, right-click a pending task and select
Cancel from the shortcut menu that appears.
• To reactive the publish process for a task that has been cancelled
or stopped due to error, right-click the task and select Restart
from the shortcut menu that appears.
Find Function
You can use the Find feature to search the process database for
samples, experiments, or experiment data (.dat, .cel, .chp), then
apply the Export, Archive, Assume Ownership or Delete
command to the objects returned by the search. The action affects only
the selected objects and does not affect related children objects.
The Find function searches only the process database.
1.
Click the Find button ; or
Select Tools → Find from the menu bar.
The Find window appears (Figure 15.25).
The Find window has three tabs:
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- Select Object
- Advanced Filter
- Date Filter
All three Find tabs work in union. For example, if you select sample
(object type) in the Select Object tab, then only the boxes that
pertain to finding samples will be active in the Advanced Filter tab.
You may open multiple Find windows.
Figure 15.25
Find window
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Select Object tab
Data Filter tab
Advanced Filter tab
Figure 15.25
Find window
Click the Select Object, Advanced Filter, or Data Filter tab and
make selections from the drop-down lists, or enter text for the
search.
Further refine your search by specifying additional search
parameters in the other Find tabs.
3. Click Find Now.
The search results are displayed at the bottom of the window
(Figure 15.26).
2.
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Figure 15.26
Find window, search results displayed
To sort the search results, choose a column header to define the
primary sort order. Click the column header to sort the results in
ascending order. Click the header again to sort in descending
order.
5. To apply the Export, Archive/Unarchive, Delete, or Assume
Ownership command to the returned search objects:
4.
A.
Select the objects for the command.
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To select adjacent objects, press and hold the Shift key, and
click the first and last object in the selection. To select nonadjacent objects, press and hold the Ctrl key while you click the
objects of interest.
B. Right-click the selection and choose the command that you
want to apply in the shortcut menu that appears (Figure 15.26);
or
Select the command from the Find menu in the menu bar.
When you apply a command to selected search results, the
command affects only the selected objects and does not affect any
associated data (related children objects).
Filtering Samples
You can filter the samples that are displayed in the Process tab data
tree (Figure 15.27). Sample filters are available in the Process or
Import tab when you click a subfolder of the Samples directory. The
filters remain active from session to session until the parameters are
changed.
In the data tree, click the Samples folder and the assay folder (for
example, Expression).
The data tree displays the samples and the Filter button
becomes available.
2. Click the Filter button
.
The Sample Filter dialog box appears (Figure 15.27).
3. Select filter parameters from the drop-down boxes.
The Role and User filter options are mutually exclusive. You may
select one or the other, but not both.
1.
4.
Click Apply.
The sample filters are applied to the data tree.
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Specify sample
filters that
determine the
samples displayed
Figure 15.27
Selections in the Sample Filters dialog box (top) determine the samples displayed in the process pane data
tree (bottom)
Publish Tab
In the Publish tab you can create new publish databases and delete
published data from a database. This section of the manual explains
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the layout of the Publish tab window, its functions, and how to
accomplish tasks here.
• Click the Process tab.
The three Process tab windowpanes are displayed (Figure 15.28).
Create
database
Database tree
This pane is
blank until
you initiate
a create
database
command.
Task status/
Properties
Figure 15.28
Publish tab windowpanes
You can learn more about the Publish tab in the following sections:
• Publish Tab Windowpanes (see below)
• Publish Tab Functions (see page 383)
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PUBLISH TAB WINDOWPANES
The Publish tab window (Figure 15.28) has the following panes:
Publish database Displays a tree that shows the active server, the publish databases on
tree
the server, and the supported probe array types and their contents
experiment data and analysis data (.cel, .chp) that have been
published for that probe array type).
Create database
Shows the Create Database dialog box when you initiate a create
database command.
Task Status/
Properties pane
Displays the status of processes that may be occurring in the
database (for example, export, import, delete, archive, or create). In
the task status view, you can monitor these jobs while you work on
other tasks in the system.
PUBLISH TAB FUNCTIONS
The primary tasks in the Publish tab are:
• Access a publish database (see page 384)
• Delete a probe array type from the publish database
(see page 385)
• Delete data from the publish database (see page 386)
• Create a publish database on the workstation or GCOS Server
(see page 388)
The tasks associated with a publish database, published data, or a
probe array type are found under Publish in the menu bar; or
Right-click an item to view a shortcut menu that appears
(Figure 15.29).
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Figure 15.29
Publish tab shortcut menus
Accessing a Publish Database
Each publish database is password protected. The password is defined
during the creation of the database. You can change the password for
a database on the GCOS server using the GCOS Server Sync utility.
(For more information on the GCOS Server Sync utility, see the
Affymetrix® GeneChip® Operating Software Server Installation and
Administration Guide.)
In the publish pane, click the database that you want to access.
A Publish Database Login window appears (Figure 15.30).
2. Enter the database password and click Login.
1.
Passwords are case-sensitive.
The publish database tree expands and displays the Probe Array
Type folder (Figure 15.30).
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Figure 15.30
Publish Database Login box
Deleting a Probe Array Type
Probe array types that are no longer used may be removed from a
publish database. When you delete a probe array type, all of the
associated published data (from the parent down) are also deleted.
Click the Probe Array Type folder under the publish database of
interest.
2. Right-click the probe array type that you want to delete and select
Delete from the shortcut menu that appears; or
Click the probe array type and select Publish → Delete from the
menu bar.
A warning window appears (Figure 15.31).
1.
Figure 15.31
Probe array delete warning/confirmation box
3.
Click Yes to continue.
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The probe array type and all associated data are removed from the
publish database.
Deleting Published Data
Deleting publish data removes selected cell intensity or probe analysis
data from the publish database. When you delete published data, all
children data are also removed.
Deleting publish data permanently removes the data from the
publish database. If the information still resides on the process
database, the data can be restored to the publish database by
repeating the publish procedure in GCOS.
In the server drop-down list, select the server where the publish
database resides.
2. In the publish pane, select the database of interest and expand the
tree.
3. Right-click the data that you want to delete and select Delete
from the shortcut menu that appears; or
Click the data and select Publish → Delete from the menu bar.
4. On the menu bar select Publish → Delete.
A warning/confirmation box appears (Figure 15.32).
1.
Figure 15.32
Analysis delete warning / confirmation window
5.
Click Yes to continue.
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The Delete task proceeds.
The task status/properties pane displays the status of the delete
task.
To view more information about the delete task status, right-click
in the Task Status/Properties pane and select View Task
Log from the shortcut menu that appears (Figure 15.33); or
Double-click
to view the delete task log (Figure 15.34).
Figure 15.33
Task Status/Properties pane
Figure 15.34
Delete task log
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Creating a Publish Database
In the Publish tab, you can create a new publish database. Table 15.11
shows the location, size, and storage capacity options for a publish
database.
Along with the new database, GCOS Manager also creates the ODBC
DSNs that are required for publishing data. Several key pieces of
information are needed to create a publish database, including:
• the server where the database will reside
• a username and password with appropriate permissions for
creating databases on the selected server
• the database size
• the proper drive and path for the database files
The server name is represented by an ODBC data source name
description. This ODBC DSN specifies the location of an
administration database that is used to create the actual publish
database. This DSN is usually created during installation of the
software.
The initial size of a Microsoft® SQL Server 2000 publish database on
the GCOS server can range from 128 to 1024 MB. The size can easily
be increased after the database is created. For information on
increasing the size of a publish database on the GCOS server, see the
GCOS Server Administration and Installation Guide.
A MSDE publish database on the workstation has a 2 GB size limit. If
the database reaches this limit, create a new publish database.
MSDE cannot create a publish database on a network drive.
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Table 15.11
Publish database location, size, and storage capacity options
Publish Database/ Size Options
Location
Storage Capacity*
Microsoft® MSDE/
workstation
8 MB per experiment (includes
experiment information, .cel, .chp)
up to 2 GB
8 MB per library file
128 MB database = 4 library files & 12
experiments
Microsoft® SQL
Server 2000/GCOS
server
128-1024 MB
initial size
range
8 MB per experiment (includes
experiment information, .cel, .chp)
8 MB per library file
128 MB database = 4 library files & 12
experiments
1024 MB database = 16 library files &
110 experiments
Oracle®/GCOS
server
* Based
Small (~6 GB)
Large
~500 experiments
~1000 experiments
on a probe array with 270x270 features, 1800 probe sets per array.
Creating a Microsoft® MSDE Publish Database on the
Workstation
Select the server where the publish database will reside from the
drop-down list on the toolbar (Figure 15.35).
2. In the publish pane, right-click the server name in the data tree
and select Create MSDE Database from the shortcut menu that
appears; or
Click the server name and select Publish → Create MSDE
Database from the menu bar.
The Create Database dialog box appears (Figure 15.35).
1.
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Select the server for the
publish database
Create Database dialog box
Database tree
Figure 15.35
Publish tab, create a MSDE publish database
3.
In the Create Database dialog box:
A.
Enter a name for the new database.
The database name is limited to 22 characters in length.
Enter a password for the database. Re-enter the password to
confirm it.
The publish database can only be accessed with this password.
4. To select the path for the database, do either of the following:
- Enter the path for the publish database
- Click Browse and select a folder from the Choose Folder
dialog box (Figure 15.36).
B.
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Figure 15.36
Choose Folder dialog box
5.
Click Install.
It takes several minutes to create the database and allocate the
amount of drive space requested (2 -15 minutes or more,
depending on the speed of the workstation and drive).
Once it is created, the database is available for publishing without
further configuration.
Creating a Microsoft® SQL Server 2000 Publish Database on the
GCOS Server
1.
Select the server where the publish database will reside from the
drop-down list on the toolbar (Figure 15.37).
2.
In the database tree, right-click the server name and select Create
SQL Server Database from the shortcut menu that appears; or
Click the server name and select Publish → Create SQL
Database from the menu bar.
The Create Database dialog box appears (Figure 15.37).
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In the Create Database dialog box:
Enter a name for the new database.
The database name is limited to 22 characters in length.
B. Enter a password for the database. Re-enter the password to
confirm it.
The publish database can only be accessed with this password.
A.
Select the server for the publish database
Database tree
Figure 15.37
Publish tab, create a Microsoft® SQL Server publish database
Create Database dialog box
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4.
393
Enter the following information in the Data device, Index
device, and Log device sections:
- Path: Use the complete drive description, including the drive
letter, colon, and backslash (for example, E:\Affymetrix
DBDevices).
The drive letter specifies the drive on the actual publish database
server. If you are creating the publish database on a remote server,
make sure the selected drive letter is available on that server.
- Size (MB): The size depends on the number of experiments
that will be published to the database and the amount of
available space on the selected drive. A Microsoft® SQL Server
database is easy to expand after creation; therefore, creating a
smaller database and expanding it as necessary is
recommended.
5.
Click Install.
It takes several minutes to create the database and allocate the
amount of drive space requested (12-15 minutes or more,
depending on the speed of the server and drive).
Once created, the database is available for publishing without
further configuration. If the new database does not appear in the
data tree, verify that the database and ODBC DSN were created
properly.
Creating an Oracle® Publish Database on the GCOS Server
An Oracle® publish database is much larger than the default Microsoft
SQL Server database. Before you create an Oracle database, verify that
there is adequate space available on the server. The small size Oracle
publish database requires 6 GB and the large size requires 12 GB.
These sizes have capacity for approximately 500 and 1,000 published
experiments respectively.
1.
Select the server where the publish database will reside from the
drop-down list on the toolbar (Figure 15.38).
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2.
In the database tree, right-click the server name in the data tree
and select Create Oracle Database from the shortcut menu that
appears; or
Click the server name and select Publish → Create Oracle
Database from the menu bar.
The Create Database dialog box appears (Figure 15.38).
3.
In the Create Database dialog box:
Enter a name for the new database.
The database name is limited to 22 characters in length.
B. Enter a password for the database. Re-enter the password to
confirm it.
The publish database can only be accessed with this password.
A.
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Select the server for the publish database
Create Database dialog box
Figure 15.38
Publish tab, create Oracle® database
4.
In the Data Device section enter the following information:
- Server Device Path: This is the complete path for the
database files. Use the complete drive description for
Microsoft® Windows® 2000 (for example, E:\Affymetrix
DBdevices\). Be sure to include the trailing slash.
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The data file path directly specifies the file location on the actual
publish database server. If you are creating a publish database on a
remote server, make sure the specified path is available on that
server.
The data file path directory used specifies the file location on the
actual publish database server. If the publish database is being
created on a remote server, make sure the path specified is
available on that server.
- Database Size: make a selection from the drop-down list.
The Small database requires approximately 6 GB of drive
space and the Large requires approximately 12 GB.
5.
Click Install.
It takes several minutes to create the database and allocate the
amount of drive space requested (15 - 30 minutes or more,
depending on the speed of the server and drive).
Once it is created, the database is available for publishing without
further configuration. If the newly created database does not
appear in the data tree, verify that the database and the ODBC
DSN were created properly.
Import Tab
In the Import tab you can copy experiment data (.exp, .cel, .chp
created in MAS 5.x) into the GCOS or GCOS server process database.
This section of the manual explains the layout of the Import tab
window and how to accomplish tasks here.
• Click the Import tab.
The four windowpanes of the Import tab are displayed
(Figure 15.39).
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Active
server
Staging area
Available data
Sample tree
Task status/
Properties
Figure 15.39
Import tab windowpanes
You can learn more about the Import tab in the following sections:
• Filtering Samples (see page 397)
• Import Tab Windowpanes (see page 400)
• Importing Data (see page 400)
FILTERING SAMPLES
You can filter the samples that are displayed in the sample tree
(Figure 15.39). Sample filters are available in the Import or Process
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tab when you click a subfolder of the Samples directory. The filters
remain active from session to session until the parameters are changed.
1.
In the sample tree, click the Samples folder and the assay folder (for
example, Expression).
The sample tree displays the samples and the Filter button
becomes available.
Click the Filter button .
The Sample Filter dialog box appears (Figure 15.27).
3. Select filter parameters from the drop-down boxes.
The Role and User filter options are mutually exclusive. You may
select one or the other, but not both.
4. Click Apply.
The sample filters are applied to the data tree.
2.
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Specify
sample
filters that
determine
the
samples
displayed
in the
sample
tree.
Figure 15.40
Selections in the Sample Filters dialog box (top) determine the samples displayed in the sample data tree
(bottom)
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IMPORT TAB WINDOWPANES
The Import tab window (Figure 15.39) has the following panes:
Sample tree
Shows the active server, process database, and samples in the system.
Staging area
Shows the sample(s) that will be associated with experiment data for
import.
Data
available for
import
Displays the experiment data located at the defined import data path.
Task status/
properties
status/
Properties
Displays the property information or local task view, depending on the
item selected in process database tree or the selected data pane. Property
information is defined by the template that was used during sample
registration in GCOS. The task status view shows the status of processes
that may be occurring in the database (for example, export, import,
delete, archive, or create). In the task status view, you can monitor these
jobs while you work on other tasks in the system.
IMPORTING DATA
The Import function imports or copies experiment data created in
MAS 5.x and moves them to a process database on the workstation or
a GCOS server. You can import data to multiple GCOS servers.
Importing data is a three-step process:
Select the data path that specifies the location of the MAS 5.x
experiment data (.exp, .dat, .cel, .chp) that you want to import (see
Selecting an Import File Path, on page 401).
2. Create a new sample or select an existing sample to associate with
the experiment data (the data will be also be associated with the
project specified by the sample information) (see Specifying a Sample
for Imported Data, on page 402).
3. Associate the experiment data with the selected sample so that
GCOS Manager can track the data in the process database (see
Associating Data & Samples, on page 408).
1.
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Selecting an Import File Path
1.
Click the data path button ; or
Select Tools → Data Path from the menu bar.
The Select Import Data Path dialog box appears (Figure 15.41).
Figure 15.41
Select Import Data Path dialog box
Make a selection from the Drives from the drop-down list and
navigate to the data that you want to import.
3. Click OK.
The defined data path and the experiment data at that location are
displayed in the available data windowpane (upper right) in the
Import tab (Figure 15.42).
2.
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Import data
Figure 15.42
Import tab, available data windowpane shows data available for import at the
current import data path
The default data path is the same path assigned to Affymetrix®
GCOS experiment data.
Specifying a Sample for Imported Data
The experiment data for import are not associated with a sample or
project. You must associate the data with a sample and a project so
that GCOS Manager can track the data in the process database. You
can associate the imported data with a new sample or an existing
sample.
Creating & Editing a New Sample
1.
Right-click the appropriate assay folder (for example, Expression)
in the process database tree and select Create Sample from the
shortcut menu that appears; or
Click the assay folder and select Import → Create Sample from
the menu bar.
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The Create Sample dialog box appears (Figure 15.43).
Table 15.12 and Table 15.13 list the data entry rules for the fields in
the Create Expression Sample dialog box.
Table 15.12
Rules for data input
Data Input
Rule
Character length
< 64 characters
Invalid characters
\ / : * ? “ < > | ‘ ~ ´, { } [ ]
Required data fields
Required fields are indicated by blue titles and may
not be left blank.
Data fields
A name may not duplicate an existing name.
Table 15.13
Valid field lengths
Sample
Attribute
Length
(characters)
Sample project
64
Sample type
64
Description
64
Comments
64
Sample name
64
2.
Enter the following required information (or make selections from
the drop-down lists):
- Sample name
- Sample project name
- Sample type
3.
Enter any descriptions or comments.
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If the sample name, project name, and sample type do not match
the information stored in the experiment file, the software notifies
you and directs you to the import log to determine inconsistencies.
4.
Click OK.
The new sample appears in the import staging area (middle pane).
Staging
area
Figure 15.43
Import tab window and Create Sample dialog box
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If necessary, you can edit the information for a new sample before you
start the data import.
The sample name cannot be edited. You can only edit a new sample
prior to data import. After data import, a sample cannot be edited.
Samples created in GCOS cannot be edited.
5.
To edit the sample information prior to data import:
A.
Right-click the sample name and select Edit from the shortcut
menu that appears (Figure 15.44); or
Click the sample name and select Import → Edit from the
menu bar.
The Create Sample dialog box appears (Figure 15.43).
Figure 15.44
Sample for imported data, shortcut menu
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B.
Enter the new information in the Create Sample dialog box and
click OK when finished.
Selecting an Existing Sample
1.
In the process database tree, expand the sample folder and click the
sample of interest (Figure 15.45).
2.
Drag the sample to the staging area.
The sample and all of the associated data are displayed with red
check marks that indicate the data already exist in the database.
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Data available for import
Staging
Area
Figure 15.45
Import tab, drag an existing sample to the Staging Area
Removing a Sample From the Staging Area
You can remove samples from the Staging Area.
• Right-click the sample that you want to remove, and select
Remove (for new samples) or Remove All (for existing samples)
from the shortcut menu that appears (Figure 15.44); or
Click the sample and select Import → Remove or Import →
Remove All from the menu bar.
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A new sample or an existing sample and its children files are
removed from the staging area.
Associating Data & Samples
The last step in the import process is to associate the experiment data
(.cel, .chp) with a sample. You can only associate data from probe array
types installed in the process database. If you attempt to associate data
from a probe array type that is not installed in the process database, an
error is displayed.
The names of imported data must conform to the naming
conventions in GCOS (see Table 15.13 on page 403). If necessary,
rename a file so that the name complies with the naming
conventions.
Associating .exp with a Sample
In the available data pane (Figure 15.46), the EXP tab displays the
experiment data (.exp) available for import at the designated data
import path. When you associate an experiment (.exp) with a sample,
the .dat, .cel, and .chp with the same prefix (if they exist) are also
automatically associated with the sample.
To associate a .exp with a sample, drag the data to the sample in
the staging area (Figure 15.46).
The .exp is added to the below the sample along with the .cel and
.chp with the same prefix (Figure 15.47).
2. To associate another .exp and its children data with the sample,
repeat step 1.
1.
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File path that specifies location of
experiment data available for import
Staging area
Figure 15.46
Import tab, drag the .exp to associate it with a sample in the staging area
Available
data
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Figure 15.47
Staging Area showing N004.exp and children data associated with sample N008
Associating Additional .cel or .chp with a Sample
You can associate additional .cel or .chp that have different prefixes
with a sample that is already associated with an .exp. This is done in a
hierarchical manner by adding the .cel to the .exp that is associated
with the sample of interest, and adding the .chp to the .cel.
To associate a .cel with a sample:
Select the CEL tab in the available data pane.
2. Drag the .cel to the .exp that is associated with the sample of
interest in the staging area (Figure 15.48). Repeat this step to
associate another .cel with the sample.
The .cel is displayed below the .exp (Figure 15.49).
To associate a .chp with a sample:
1.
1.
Select the CHP tab in the available data pane.
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411
Drag the .chp to the .cel that is associated with the sample of
interest in the staging area. Repeat this step to associate another
.cel with the sample.
The .chp is displayed below the .cel (Figure 15.49).
To avoid having to associate a .cel and .chp with each .exp imported
into the process database, simply import the .exp, then regenerate
the.cel and .chp in GCOS using batch analysis. This minimizes
potential errors from dragging a .chp to the wrong .cel. For more
information, see Chapter 11, Batch Analysis, on page 297.
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Staging area
Figure 15.48
Import tab
Available data
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Additional .cel and .chp with
different prefixes that are
associated with sample N008
Figure 15.49
Staging area showing .cel and .chp data associated with the sample N008
Removing Data from the Staging Area
You can remove experiment data (.exp, .cel, or .chp) from the staging
area. Use either of the following methods to remove data:
• Right-click the sample that you want to remove, and select
Remove (for data without children) or Remove All (for data and
associated children data) from the shortcut menu that appears
(Figure 15.44); or
Click the sample and select Import → Remove or Import →
Remove All from the menu bar.
The selected data or data and children data are removed from the
staging area.
• Drag the data from the staging area to the available data pane.
This must be done in an ascending hierarchical manner by
dragging the .chp to the CHP tab, the .cel to the CEL tab, and the
.exp to the EXP tab.
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Starting the Import
1.
Right-click the process database, a sample, or one of the data items
and select Start Import from the shortcut menu that appears; or
Click one of these items and select Import → Start Import from
the menu bar.
The import task proceeds and the task status/properties pane
displays the import status.
2.
To view more information about the import task status, right-click
in the Task Status/Properties pane and select View Task
Log from the shortcut menu that appears (Figure 15.50); or
Double-click
.
The import task log is displayed (Figure 15.51).
Figure 15.50
Task Status/Properties pane
Figure 15.51
Import task log
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Userset Tab
This section of the manual explains how to create, modify, or delete a
userset. A userset is a set of modifiable Statistical Expression
algorithm parameters with predefined values. For more information
about the expression algorithm parameters, see Expression Analysis
Algorithm, on page 627.
A userset is defined by an administrator or other authorized user. It
provides a convenient way to select analysis parameters without
having to set each parameter individually before an analysis. A userset
is applied in GCOS when you analyze expression cell intensity data.
You can learn more about the Userset tab in the following sections:
• Userset Tab Windowpanes (see below)
• Creating a Userset (see page 417)
• Modifying a Userset (see page 421)
• Deleting a Userset (see page 424)
USERSET TAB WINDOWPANES
• Click the Userset tab.
The three Userset windowpanes are displayed (Figure 15.39).
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Create/Update pane
Userset tree
Task status/
Properties
Figure 15.52
Userset tab windowpanes
The Userset tab window (Figure 15.52) has the following panes:
Userset tree
Shows the active server, process database, user sets and associated
probe array types.
Create/
Shows new userset information that can be specified or existing userset
Update pane information that can be modified (Figure 15.53).
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Task status/
properties
417
Displays the property information or local task view, depending on the
item selected in process database tree or the selected data pane.
Property information is defined by the template that was used during
sample registration in GCOS. The task status view shows the status of
processes that may be occurring in the database (for example, export,
import, delete, archive, or create). In the task status view, you can
monitor these jobs while you work on other tasks in the system.
Probe array types included in an
existing userset. Or probe array
types to include in a new user set
Probe array
types in the
process
database
Existing
userset
names
New
userset
name
Independent
parameters
Dependent
parameters
Figure 15.53
Create/Update pane
CREATING A USERSET
Creating a userset includes the following steps:
1.
Enter a name for the userset.
2.
Select the probe array type(s) that the userset will analyze.
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Confirm the defaults or enter new values for the independent
parameters.
4. Confirm the defaults or enter new values for the dependent
parameters.
To create a userset:
3.
In the Create set name box, enter a unique name for the userset.
2. In the Probe array types box, select a probe array type and click
the arrow button >>. Repeat this step to add other probe array
types for the userset.
The selected probe array type(s) is displayed in the Probe array
types used box and the independent and dependent parameters
are set to the default values (Figure 15.54).
3. If you want to use the independent and dependent parameter
defaults, click Create Set.
The userset is created and the name appears in the Existing
userset name(s) box.
If you do not want to accept the defaults, see the following sections
on modifying the independent and dependent parameters.
1.
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Dependent parameters
419
Independent parameters
Figure 15.54
Create/Update pane
Modifying Independent or Dependent Parameter Values
The statistical expression algorithm parameter settings are
independent parameters. These are static settings that are not
influenced by the probe array type.
A dependent parameter is a setting that is specific to a particular probe
array type. Dependent parameters include the scaling, normalization,
probe mask, and baseline settings. For more information on these
parameters, see Expression Analysis Settings, on page 644.
1.
To modify an independent parameter:
A.
In the independent parameters box, click the parameter that
you want to modify.
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The parameter name and current setting are displayed in the
box above (Figure 15.55).
Current
value for the
selected
independent
parameter.
Enter a new
value here.
Figure 15.55
Create/Update pane
Enter a new value in the box and click Modify.
The new parameter value is displayed in the box below.
C. Repeat step b to modify other independent parameters.
2. To modify a dependent parameter:
B.
Click the tab for the parameter you want to modify (Scaling,
Normalization, Probe Mask, or Baseline).
B. Choose the analysis option that you want to include in the
userset and enter any additional necessary information.
A.
3.
Click Create Set after you finish modifying the parameter values.
The userset is created and the name appears in the Existing
userset name(s) box (Figure 15.55).
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The new parameter values are applied after you click Create Set.
MODIFYING A USERSET
You can modify the independent or dependent parameter values for a
userset, or add or remove a probe array type(s) from a userset.
1.
In the Existing userset name(s) box, click the userset that you
want to modify.
The Create/Update pane shows the parameter values for the
selected userset (Figure 15.56).
Figure 15.56
Create/Update pane
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2.
To add a probe array type to the userset, select a probe array type
in the Probe array types box, and click the arrow button >>.
Repeat this step to add other probe array types for the userset.
The selected probe array type(s) is displayed in the Probe array
types used box (Figure 15.56).
3.
To remove a probe array type from the userset, do either of the
following:
- Select a probe array type in the Probe array types used box,
and click the arrow button <<.
The selected probe array type is removed from the Probe array
types used box.
- In the userset tree, expand the Statistical folder and the userset
that you want to modify. Right-click the probe array of
interest and select Delete from the shortcut menu that appears
(Figure 15.57).
If you remove a probe array type from the process database in the
Process tab, the probe array is also removed from any userset that
includes this array type in its Probe Array Types Used list.
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Figure 15.57
Userset tab window
4.
To modify an independent or dependent parameter value, see the
section Modifying Independent or Dependent Parameter Values, on
page 419.
5.
Click Update Set after you finish modifying the userset.
The modifications are saved to the userset and the task status/
properties pane displays the Statistical Expression algorithm
properties (Figure 15.58).
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Figure 15.58
Task Status/Properties pane
This information is metadata that exists in the process database and is
used internally by GCOS and the GCOS server to distinguish different
algorithms in the system.
DELETING A USERSET
1.
In the userset tree, right-click the userset that you want to delete
and select Delete from the shortcut menu that appears; or
Click the userset and select Userset → Delete from the menu bar.
A warning/confirmation box appears (Figure 15.59).
Figure 15.59
Delete userset warning/confirmation box
2.
Click Yes to delete the userset.
The userset is removed from the userset tree and the Existing
userset name(s) box in the create/update pane.
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Template Tab
A template is a form that defines the attributes and values needed to
register a sample or set up an experiment in GCOS. A sample or
experiment template is created by the administrator or other
authorized user. This section of the manual explains how to create and
manage sample or experiment templates.
You can learn more about the Template tab in the following sections:
• Template Tab Windowpanes (see below)
• MIAME Sample Template (see page 427)
• Working with Templates (see page 428)
• Working with Attributes (see page 439)
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TEMPLATE TAB WINDOWPANES
Template tree
Attributes
This pane is blank until you select a
template in the template tree or initiate
a create template command.
Task status/
Properties
Figure 15.60
Template tab windowpanes
The Template tab window (Figure 15.60) has the following panes:
Template
tree
Shows the active server, process database, and the experiment and
sample templates that reside there. Click a sample or project to display
the associated experiments and data (.dat, .cel, .chp) in the data pane.
Select a template to display the attributes and values in the attribute pane.
Attributes
Displays the template selected in the template tree. Displays a blank
template when a Create Template command is initiated.
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Task status/ Displays the property information or local task view, depending on the
Properties item selected in process database tree or the selected data pane. Property
information is defined by the template that was used during sample
registration in GCOS. The task status view shows the status of processes
that may be occurring in the database (for example, export, import,
delete, archive, or create). In the task status view, you can monitor these
jobs while you work on other tasks in the system.
MIAME SAMPLE TEMPLATE
GCOS Manager provides a sample template based on the Minimum
Information About a Microarray Experiment (MIAME).1 The MIAME
sample template includes 23 types of sample attributes. For each
attribute, you may:
• define the data type
• specify whether the attribute information is required for sample
registration
• specify the values available for a controlled value attribute
To view the MIAME Sample Information template, click the
MIAME Sample Information template in the Sample Templates
folder (Figure 15.61).
The Attributes pane displays the MIAME Sample Information
template.
2. To enter template information, follow step 5 to step 12 in the
section Creating a Template, on page 428.
1.
1
A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball,
H.C. Causton, T. Gaasterland, P. Glenisson, F.C. P. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A.
Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R Taylor, J. Vilo, and M. Vingron. Minimum information
about a microarray experiment (MIAME)- toward standards for microarray data. Nature Genetics, 29:365-371.
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Figure 15.61
MIAME Sample Information template
WORKING WITH TEMPLATES
Creating a Template
When you create a template, you specify:
• the attributes included in the template
• the data type for each attribute (for example, an integer or a
character string)
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• whether the attribute is required
• value options for a controlled data attribute
1.
To create an experiment template, right-click the Experiment
Templates folder and select Create from the shortcut menu that
appears; or
Click the folder and select Template → Create from the menu bar
(Figure 15.62).
To create a sample template, right-click the Sample Templates
folder and select Create from the shortcut menu that appears; or
Click the folder and select Template → Create from the menu
bar.
The Create Template box appears (Figure 15.63).
Figure 15.62
Template tree, shortcut menu for experiment templates
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Figure 15.63
Create Template box
2.
Enter a name for the template.
A blank template appears in the attribute pane (Figure 15.64) and
the template name is added to the appropriate folder (experiment
or sample). Click the folder and expand it to view the newly added
template name.
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Figure 15.64
Template tab, experiment template
3.
In the template, double-click the first blank cell under the Name
column.
The mouse pointer becomes an I-beam and the other cells in the
row are blocked (Figure 15.65).
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Figure 15.65
Attributes pane
4.
Enter an attribute name and press ENTER.
The attribute name is inserted and numbered (Figure 15.66).
During the process of defining an attribute, you can click Undo to
remove the entries from the Attributes pane.
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Name
attribute
inserted
Figure 15.66
Attributes pane
5.
6.
Click the cell under the Type column and click the drop-down
arrow that appears.
A drop-down list of data type options for the attribute appears
(Figure 15.66).
Integer
Whole number
Float
Floating point number
String
Limited to 255 characters
Date
Date
Time
Time
Controlled
Limits user response to the value options listed in the template.
Make a selection from the Type drop-down list.
The selected data type is displayed in the cell (Figure 15.67).
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Figure 15.67
Attributes pane
7.
Click the cell under the Required column and click the drop-down
arrow that appears.
8.
In the drop-down list that appears, click Yes if the information is
required or No if it is not (Figure 15.68).
If the information is required, GCOS requires the user to enter a
value during the sample registration or experiment set up process.
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Figure 15.68
Attributes pane
9.
If the attribute data type is controlled, double-click the cell under
the Values column.
The Controlled Values Edit List box appears (Figure 15.69).
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Figure 15.69
Attribute pane and the Controlled Values Edit List box
10. To
define a controlled value:
Enter a value option in the box.
B. Press Enter.
C. Repeat steps a and b to enter additional controlled values.
D. Click OK when finished.
The controlled values appear in the Values drop-down list
(Figure 15.70).
A.
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Figure 15.70
Attributes pane and the drop-down list of controlled values for the attribute
11. Click
Apply.
The defined attributes are now in effect.
12. To define additional attributes for the template, repeat step3
through step 11.
Editing a Template
You can edit an existing template.
In the template tree, click the template you want to edit.
The attributes pane displays the selected template.
2. To edit an attribute name, double-click the current entry and enter
a new name.
1.
3.
Follow step 3 to step 11 in the section Creating a Template, on
page 428 to edit the attribute definition.
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Deactivating or Activating a Template
You can deactivate a template to make it unavailable in GCOS. An
inactive template can be activated to restore it for use in GCOS.
1.
To deactivate a template:
Right-click the template of interest in the template tree and
select Deactivate from the shortcut menu that appears; or
Click the template and select Template → Deactivate from
the menu bar.
B. Click OK in the warning window that appears.
The template icon appears gray in the template tree to indicate
the template is inactive and is not available to GCOS.
2. To activate a template:
A.
A.
Right-click the template of interest in the template tree and
select Activate from the shortcut menu that appears; or
Click the template and select Template → Activate from the
menu bar.
The template icon is restored to full color in the template tree
to indicate the template is active and is available to GCOS.
Renaming a Template
1.
In the template tree, right-click the template that you want to
rename and select Rename from the shortcut menu that appears;
or
Click the template and select Template → Rename from the
menu bar.
2.
Enter a name for the template and press ENTER.
You cannot duplicate an existing name for the same type of
template.
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WORKING WITH ATTRIBUTES
To view a shortcut menu of attribute commands:
• Right-click an attribute number (Figure 15.71); or
Click an attribute number and select Template → Attribute from
the shortcut menu that appears.
Attribute
number
Figure 15.71
Attributes pane, shortcut menu
To select an attribute for a command:
• Click the attribute number.
To select a group of adjacent attributes:
• Press and hold the Shift key while you click the number of the
first and last attribute in the group.
To select non-adjacent attributes:
• Press and hold the Ctrl key while you click the attribute
numbers.
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Inserting an Attribute
You can insert a blank row in the template.
1.
Right-click the attribute number below the insertion point and
select Insert from the shortcut menu that appears; or
Click the attribute number and select Template → Insert from
the menu bar.
A blank row is inserted in the template.
2.
Define the attribute and click Apply.
Deactivating an Attribute
A deactivated attribute is not displayed in the template for sample
registration or experiment setup in GCOS.
Right-click the number of the attribute that you want to
deactivate and select Deactivate from the shortcut menu that
appears; or
Click the attribute number and select Template → Attribute →
Deactivate from the menu bar.
The attribute remains in the template, but appears grayed-out.
2. Click Apply.
A warning message appears.
3. Click OK to deactivate the attribute.
1.
In GCOS, the attribute is displayed in samples and experiments that
were saved using the attribute. These cannot be modified. A
deactivated attribute is not available for new samples or
experiments.
Activating an Attribute
1.
Right-click the number of the attribute that you want to activate
and select Activate from the shortcut menu that appears; or
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Click the attribute number and select Template → Attribute →
Activate from the menu bar.
The attribute is no longer grayed-out.
2. Click Apply.
The attribute becomes active and is available in the template.
Cutting, Copying or Pasting an Attribute
1.
To cut an attribute, right-click the attribute number and select
Cut from the shortcut menu that appears; or
Click the attribute number and select Template → Attribute →
Cut from the menu bar.
The attribute information is copied to the system clipboard.
To copy an attribute, right-click the attribute number and select
Copy from the shortcut menu that appears; or
Click the attribute number and select Template → Attribute →
Copy from the menu bar.
The attribute information is copied to the system clipboard.
3. To paste an attribute, right-click the attribute number and select
Paste from the shortcut menu that appears; or
Click the attribute number and select Template → Attribute →
Paste from the menu bar.
The attribute information on the system clipboard is pasted on the
template at the end of the attribute list.
4. Click Apply.
2.
Roles Tab
The Roles tab is only available to GCOS users connected to a GCOS
server.
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A role is a defined set of user access privileges. The administrator or
other authorized user can create roles with different levels of access
privilege for different users or groups of users. In this way, the roles
function provides data security. This section of the manual explains
how to create and manage roles.
You can learn more about the Roles tab in the following sections:
• Roles Tab Window (see below)
• Creating a Role (see page 444)
• Defining Role Membership (see page 448)
• Deleting Roles (see page 451)
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ROLES TAB WINDOW
Roles Definitions tree
Privilege/Domain pane
Task status/
Properties
Figure 15.72
Roles tab windowpanes
The Roles tab window (Figure 15.72) has the following panes:
Role Definitions Displays the active server, the process database, the roles created on
tree
the server, and the members of each role (Figure 15.73).
Privileges pane
Displays a list of the domains that reside on the active server.
Shows the privileges that are associated with a role selected in the
role definitions tree. Displays a template of privileges that is used to
define privileges for a new role.
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Task status/
Properties
Displays the property information or local task view, depending on
the item selected in process database tree or the selected data pane.
Property information is defined by the template that was used during
sample registration in GCOS. The task status view shows the status of
processes that may be occurring in the database (for example, export,
import, delete, archive, or create). In the task status view, you can
monitor these jobs while you work on other tasks in the system.
Active server
List of role
definitions
Process database
List of member
definitions
Roll member
Figure 15.73
Role definitions tree
CREATING A ROLE
A role defines a set of user access privileges. Each GCOS user is
assigned to a role. Creating a role is a three-step process:
Name the role.
2. Define the role privileges (what the user can and cannot do).
3. Define role membership (add users to the role).
1.
Naming the Role
1.
Right-click an existing role in the role definitions tree and select
Create Role from the shortcut menu that appears; or
Click the role and select Role → Create Role from the menu bar.
The Create Role box appears (Figure 15.74).
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Figure 15.74
Create Role box
2.
Enter a name for the role and click OK.
The role name appears in the role definitions tree (Figure 15.75).
The role name is required and cannot duplicate an existing name.
Added role
name
Figure 15.75
Role definitions tree
3.
In the role definitions tree, drag the role name to the process
database.
The role is added to the list of member definitions under the
process database.
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Figure 15.76
Drag the role to the process database
Defining Privileges
1.
In the role definitions tree, click the role that you want to define.
The Privileges pane displays a template of rights and privileges
(Figure 15.77).
Figure 15.77
Default privilege settings
In the privilege template, the function list shows the privileges
that can be granted to a role member with respect to their own
data. The second column called Other User Data Access defines the
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447
rights of the role member with respect to other users’ data. Table
15.14 defines the privilege functions.
2. Click the check box next to a function to select that privilege for
the role with respect to the user’s own data.
3. Click Yes/No in the right column to toggle between the two
options and define the user privilege with respect to other users’
data.
Other User Data Access is always Yes and cannot be toggled for the
following functions: Take Ownership, Maintain Roles, Import
Process Data, and Delete Publish Data.
Table 15.14
Role privileges
Function
Allows a user to...
Read Process Database
Browse sample, experiment or analyses information in the process
database.
Update Process Database
Modify sample and experiment properties information in the process
database.
Update Publish Database
Overwrite experiment and analyses information in the publish database.
Archive Process Data
Archive .dat, .cel, or .chp data to an user-specified location.
Delete Process Data
Delete sample, experiment, analyses, userset and probe array type
information from the process database.
Delete Publish Data
Delete experiment and analyses information from any publish database.
Import Process Data
Migrate Affymetrix® GCOS data files into the process database.
Export Process Data
Copy sample, experiment, and analysis data from the GCOS server to a
defined location.
Take Ownership of
Process Data
Assume ownership of a sample, experiment or analysis information with
the ability to overwrite a file with new contents (for example, reanalyze a
.cel with different expression analysis parameter settings).
Maintain Roles
Manage role, role membership, and set privileges.
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Table 15.14
Role privileges
Function
Allows a user to...
Delete Server Tasks
Delete publish tasks on or before a given date.
Maintain Templates
Manage templates and their attributes.
Maintain Usersets
Manage expression analysis parameter sets.
Create Publish Database
Create a publish database.
DEFINING ROLE MEMBERSHIP
You add a user to a role in order to assign the user the privileges that
are defined for the role. You can also remove a user from a role.
Adding a User to a Role
1.
In the role definitions tree, click the role of interest in the list of
member definitions (under the process database).
The privilege/domain pane displays the domain name tree
(Figure 15.78).
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Privilege/Domain pane
Roles Definitions tree
Task status/
Properties
Figure 15.78
Roles tab, domain names
Expand the domain names and locate the user name of interest.
The tree displays the user groups that reside on the domain.
3. Drag the user name to the role of interest in the member
definitions list.
The user is added to the role and the role name displays the new
member name (Figure 15.79).
2.
Click and drag the
icon to add an entire user group to a role.
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Figure 15.79
Roles tab
Deleting a User from a Role
In the role definitions tree (under the process database), expand the
user list for the role of interest.
2. Right-click the member that you want to delete and select
Remove User from the shortcut menu that appears
(Figure 15.80); or
Click the user and select Roles → Remove User from the menu
bar.
1.
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Figure 15.80
Role definitions tree
3.
The user name is removed from the role membership.
DELETING ROLES
LIMS User and LIMS Administrator are default roles and cannot be
deleted.
1.
In the role definitions tree (under the active server), right-click the
role that you want to delete and select Delete Role from the
shortcut menu that appears (Figure 15.81); or
Click the role and select Roles → Delete Role from the menu bar.
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Figure 15.81
Role definitions tree
2.
In the warning/confirmation box that appears, click Yes to
proceed.
The role is deleted and is removed from the role definitions tree.
Chapter
16
GCOS Administrator
Chapter
16
455
GCOS Administrator
The GCOS Administrator provides tools to backup a database as well
as data and help you manage your workstation disk space. This chapter
explains how to use the GCOS Administrator to:
• Automatically backup the process database on the workstation.
• Monitor available space on a workstation drive or database.
• Relocate a publish database between workstation drives.
• Register or unregister a GCOS server.
This chapter contains the following sections:
• Getting Started (see below)
• Register or Unregister a GCOS Server (see page 459)
• Changing a Database Password (see page 461)
• Automatic Process Database Back Up (see page 462)
• Managing Workstation Databases (see page 464)
Getting Started
1.
To start the GCOS Administrator, click the Microsoft® Windows®
Start menu button
, then select Programs → Affymetrix
→ GCOS Administrator.
The GCOS Administrator starts and displays the user interface.
Figure 16.1 shows the user interface at startup when the
workstation is the active server and Figure 16.2 shows the user
interface at startup when a GCOS server is selected.
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Toolbar
Data source selected
in the server dropdown list
Space Manager
Monitors available
space on a
workstation drive or
database. Available
only when connected
to the local GCOS
MSDE database.
Figure 16.1
GCOS Administrator user interface at startup, workstation server selected
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Server drop-down list
Figure 16.2
GCOS Administrator user interface at startup, GCOS server selected
2.
To select the active server, make a selection from the server dropdown list in the toolbar.
3.
To display the Space Manager window:
Select Local from the active server drop-down list.
B. Click the Space Manager button
.
A data tree and property pane are displayed (Figure 16.3).
A.
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The Space Manager functions are only available for the workstation
database and not for a GCOS server.
Shortcut
bar
Data tree
Property pane
Space Manager window
Figure 16.3
GCOS Administrator, Space Manager window for the workstation database
You can learn more about the GCOS Administrator interface in the
following sections:
• GCOS Administrator Shortcut Bar & Windowpanes (see below)
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• Register or Unregister a GCOS Server (see page 459)
• Register or Unregister a GCOS Server (see page 459)
GCOS ADMINISTRATOR SHORTCUT BAR & WINDOWPANES
The GCOS Administrator window (Figure 16.3) has the following
panes:
Shortcut
bar
Click the Space Manager button
to display the Space Manager
window for the workstation database.
Data tree
Space Manager window (for the workstation): displays the publish
databases on the active server, workstation drives, and the locations of
the probe information (library) files and experiment data. (The file
locations are in GCOS.)
Property
pane
Space Manager window (for the workstation): displays property
information for the item selected in the data tree, the free and used space
for a selected database or drive, or directory size.
Register or Unregister a GCOS Server
GCOS Administrator can register or unregister a GCOS server. The
GCOS server can be the source of objects (a publish database or data)
that you want to backup or the destination for objects that you want
to restore. This enables the transfer of a publish database or data
between a workstation and a GCOS server.
You may have more than one registered GCOS server; however,
GCOS, GCOS Manager, and GCOS Administrator can connect to
only one GCOS server at a time.
To learn more, see:
• Registering a GCOS Server (see below)
• Unregistering a GCOS Server (see page 460)
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REGISTERING A GCOS SERVER
1.
Click the Server button ; or
Select Tools → Register GCOS Server from the menu bar.
The Register GCOS Server box appears (Figure 16.4).
Figure 16.4
Register GCOS Server box
2.
Select the server that you want to register and click OK.
The GCOS server name is added to the server drop-down list.
UNREGISTERING A GCOS SERVER
1.
Select the GCOS server that you want to unregister in the server
drop-down list (Figure 16.5).
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GCOS server
selected in the
server drop-down
list
Figure 16.5
Server drop-down list
2.
Press the Delete key or select Tools → Unregister GCOS Server
from the menu bar.
The GCOS server is unregistered and the server name is removed
from the server drop-down list.
Changing a Database Password
You can change the password for the process database or a publish
database on the workstation.
1.
Click the Password button .
The Administrator Password Dialog opens (Figure 16.6).
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Figure 16.6
Administrator Password Dialog
2.
3.
4.
5.
6.
Make a selection from the Database drop-down list.
Enter the current password for the selected database.
Enter a new password for the database.
Re-enter the password to confirm it.
Click OK.
Automatic Process Database Back Up
When the workstation is turned on, the GCOS Administrator
automatically starts and runs in the background. The system tray
displays the GCOS Administrator icon. For example, Figure 16.7
shows the GCOS application open and the GCOS Administrator
running in the background.
The GCOS Administrator monitors the number of analyses that are
added to the process database on the workstation. After every 50
analyses added to the process database, the software automatically
backs up the process database to the GCOS directory (\backup
subfolder).
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The automated backup feature is only available for a process
database on the workstation. It is not available for a process
database on a GCOS server.
System tray
GCOS Administrator icon in the system
tray indicates the application is running in
the background
Figure 16.7
GCOS application window is open and GCOS Administrator runs in the
background
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• To maximize the GCOS Administrator application, double-click
the
icon.
• To access a shortcut menu for the GCOS Administrator, rightclick the GCOS Administrator icon
in the system tray.
Shortcut Menu
Command
Function
Maximize
Maximizes the GCOS Administrator window.
Minimize
Minimizes the GCOS Administrator window.
Exit
Exit the GCOS Administrator application.
If you exit the GCOS Administrator application, the process database
will not be automatically updated.
Managing Workstation Databases
GCOS Administrator provides tools to help you manage your process
and publish databases on the workstation.
• To open the space management window (Figure 16.8), click the
Space Manager button
.
In this window, you can:
• View the properties of a workstation database, drive, or GeneChip
directory.
• Monitor free and used space on a workstation database, drive, or
directory.
• Relocate a database between workstation drives.
The Space Manager functions are only available for the workstation.
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Shortcut
bar
Data tree
Property pane
Figure 16.8
GCOS Administrator, Space Manager window
To learn more, see:
• Viewing Property & Space Information (see below)
• Relocating a Publish Database (see page 466)
• Publish Database Statistics (see page 467)
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VIEWING PROPERTY & SPACE INFORMATION
• To view information about a workstation database, drive, or
directory, click the item of interest in the data tree.
The property pane displays information about the selected item
(top) and a pie chart of space information.
Table 16.1 lists the types of information that are available.
Table 16.1
Space management information
Item
Property Pane Displays...
Database
Database files names
Physical location of the database files
Disk space allocated to each database file
Pie chart of free and used database space
Drive
Databases on the drive
Size of each database
Create date for each database
Pie chart of free and used drive space
GeneChip Data
Directory
Number of files in the directory
Directory size
Pie chart of drive size and data size
RELOCATING A PUBLISH DATABASE
GCOS Administrator can move a workstation publish database to a
user-specified drive.
In the data tree, click the publish database that you want to
relocate.
The property pane displays the location and space allocation for the
files that comprise the database (data device, log device, and index
device) (Figure 16.9).
For more information on these files, see Performance Tuning for SQL
Server Databases, on page 709.
2. In the property pane, make a selection from the Location dropdown list for the database file that you want to move.
1.
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Click outside the drop-down list (to lose focus).
The file is relocated to the selected drive.
4. Repeat Step 2 and Step 3 for each database file to be moved.
3.
Shortcut
bar
Data tree
Property pane
Figure 16.9
GCOS Administrator, Space Manager window
PUBLISH DATABASE STATISTICS
1.
To view publish database statistics, click a publish database in the
data tree.
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The property pane displays all of the databases that comprise the
publish database. For each database, it shows the:
- database name
- allocated size
- create date
- probe array type
- number of published experiments
- estimated number of experiments that can be published (with
intensity data)
- estimated number of experiments that can be published
(without intensity data)
2.
To find out how many experiments can be published using a
particular probe array type, select the array type from the probe
array drop-down list.
Appendix
A
Client Testing
Appendix
A
471
Client Testing
After installing the different client software applications, testing of
the software must be completed to verify the functionality of the
software components. Following the checklist below will complete the
testing process.
The screen captures depicted in this section may not exactly match
the windows displayed on your screen.
If you encounter problems during testing, please refer to
Appendix K, Troubleshooting, on page 715.
This appendix contains the following sections:
• GCOS Manager 1.4 Testing (see below)
• GCOS 1.4 Testing (see page 493)
• Data Mining Tool 3.1 Testing (see page 518)
• GCOS Manager Additional Testing (see page 523)
GCOS Manager 1.4 Testing
For more details about the GCOS Manager 1.4 client application, refer
to Chapter 15, GCOS Manager, on page 347.
1. To perform the testing, login to the workstation as a user who has
Administrator permissions.
2. Launch GCOS Manager 1.4 (Start → Programs → Affymetrix
→ GCOS Manager)
3. Verify that the a server is registered on the left hand side.
4. Click the Process, Publish, Import, Userset, Template and
Roles tabs to verify that they are accessible.
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The Roles tab is only available when GCOS Manager is connected
to a GCOS server.
PROCESS TAB
5. Click the Process tab.
The Process tab shows the administrator the data is in the system.
In this tab you can archive, unarchive, delete, export, assume
ownership, and print data.
6. Expand the Samples folder.
7. Verify that the Expression folder appears.
8. Expand the Expression folder. If this is an upgrade, existing
samples should appear.
PUBLISH TAB
9. Click the Publish tab
In this tab, users with access can create new publish databases or
delete published data in any publish database on the system.
10. In the Publish tab, highlight the name of the active server.
11. Go to the menu bar and select Publish → Create SQL Server
Database (if using SQL Server). If using Oracle®, go to step 16.
You can create a publish database on the workstation by following
the steps for creating a database on a SQL server.
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Figure A.1
Create SQL Server Publish Database window
12. Enter the following information:
Database
- Database Name - The name of the publish database to be
created (in this example, MyPub).
- Database Password - Enter password for access to the publish
database.
- Confirm Database Password - Re-enter password for
confirmation.
The publish database is password protected. To access a publish
database, users are required to enter the appropriate password.
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Data Device
- Path – Full path location for the Data Device to reside on the
GCOS server (for example, F:\GeneChipDBDevices).
- Size – Size of the Data Device (128MB).
Index Device
- Path – Full path location for the Index Device to reside on the
GCOS server (i.e. F:\GeneChipDBDevices).
- Size – Size of the Index Device (128MB).
Log Device
- Path – Full path location for the Log Device to reside on the
GCOS server (for example, F:\GeneChipDBDevices).
- Size – Size of the Log Device (128MB).
The Microsoft® SQL Server database that you create must be
between 128MB to 1024 MB. If you want to expand the size after
the database is created, use SQL Enterprise Manager to expand the
database.
13. Click Install after all information is entered.
This may take a few minutes depending on the size of the
database created.
Creating a Publish database only needs to be tested once from a
client. It does not need to be tested on additional clients, as publish
databases are quite large. The path location for the devices must
already exist on the server, otherwise creating the database will
fail.
14. Click Close when the database is created.
15. Go to Step 19.
16. To create an Oracle® publish database, select
Publish → Create Oracle Database from the menu bar.
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The Create Oracle Publish Database window appears (Figure A.2).
You can create an Oracle publish database when the GCOS
Manager is connected to a GCOS server running Oracle.
Figure A.2
Create Oracle® Publish Database window
17. Enter the following information:
Database:
- Database name – Name of the Publish database (in this
example, MyPub)
- Database password – Enter password for access to publish
database
- Confirm database password – Re-enter password for
confirmation
The publish database is password protected. To access a publish
database, users will be required to enter the appropriate password.
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Data Device:
- Server device path – Full path location for the Device to
reside on the GCOS server (for example,
D:\GeneChipDBDevices\)
- Database size – Small or Large (in this example, select Small)
The server device path directory specifies the file location on the
actual publish database server. If the publish database is being
created on a remote server, make sure the path specified is
available on that server.
An Oracle® publish database is much larger than the default SQL
Server database. Verify that there is adequate space on the server
before creating an Oracle database. The Small Oracle publish
database requires 8GB of hard disk space. The Large Oracle publish
database requires 17 GB of hard disk space. These database sizes
correspond to publishing approximately 500 and 1000 experiments
respectively. Creating an Oracle database will take a while.
18. Click Close after the database is created.
You only need to test creating a publish database once from a
client. You need not repeat the test on additional clients, as a
publish database is quite large.
IMPORT TAB
19. Click the Import tab.
The Import function copies or imports experiment data created in
GCOS and moves the data to a process database on the workstation
or GCOS server.
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20. On the menu bar, select Tools → File Path. Set the path for the
location of the files for import. For example,
C:\GeneChip\TempData (Figure A.3).
Figure A.3
Select Import File Path window
21. Click OK.
22. Highlight the Expression Folder. From the menu bar, select
Import → Create Sample.
The Create Expression Sample window appears (Figure A.4).
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Figure A.4
Create Expression Sample window
23. Enter the following information:
- Sample Name: ImportSample
- Sample Project: MySampleProject
- Sample Type: MySampleType
- Description: <optional>
- Comments: <optional>
The fields in blue are required fields.
24. Click OK.
GCOS Manager can import any data for which a library file has been
installed. To preserve the experiment information, all data in the
sample name, project, and array type should match the data in the
experiment file.
25. Select the .exp file and drag it to the sample in the Data to
import pane (Figure A.5).
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Figure A.5
Importing .exp data
The .exp file brings all associated files with the same prefix when
placed on the sample (Figure A.6).
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Figure A.6
Importing .exp brings associated files
26. If there are additional .cel or .chp files associated with this
experiment, select the CEL or CHP tab and drag the appropriate
file to the sample in the Data to import pane.
27. When all of the files for the import are associated with a sample,
select Import → Start Import from the menu bar; or
Right-click any file in the Data To Import pane and select Start
Import from the shortcut menu that appears.
28. If the import fails, check the import status in status pane.
Double-click Import in Task View and review the error message.
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USERSET TAB
29. Click the Userset tab.
In this tab you can create a userset that defines values for the usermodifiable expression algorithm parameters. You can select the
userset by name to analyze experiments using the same set of
algorithm parameter settings.
Figure A.7
Upper right pane of the Userset tab
30. Enter a name for the set in the Create Set Name field (enter
MySet).
31. Select the Probe Array Type (Hu6800) in the Probe Array Types
Used field and move it by pressing >>. (Only one probe array
type can be moved at a time.)
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32. Click Create Set. The userset is created and the userset name is
added to the right hand side of the pane.
TEMPLATE TAB
Template attributes cannot be deleted, only deactivated. A
template can be deleted (right-click the template and select Delete
from the shortcut menu that appears).
33. Click the Template tab.
In this tab the administrator can add fields to the Experiment
Template and the Sample Template that are used in GCOS.
34. To create an Experiment Template, highlight the Experiment
Templates Folder.
35. Select Template → Create from the menu bar. (If it is grayed
out, highlight the Experiment Templates Folder again, or rightclick the Experiment Template Folder and select Create from the
shortcut menu that appears) (Figure A.8).
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Figure A.8
Template Tab window
The Create Template box appears (Figure A.9).
Figure A.9
Create Template box
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36. Enter the name of the template (for example, exp_temp). Click
OK.
The experiment template attributes window appears in the upper
right pane (Figure A.10).
Figure A.10
Experiment Template Attributes window
37. Double-click in the Name field to get a blinking cursor.
38. Enter Comments in the Name field.
39. Select String in the Type field.
40. Select No in the Required field.
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Figure A.11
Attributes and values entered
41. Click Apply.
The Exp_Temp experiment template is added to the Experiment
Templates list.
(You must select the Experiment Templates folder to see the newly
added template.)
42. To create a Sample Template, highlight the Sample Templates
Folder.
43. Select Template → Create from the menu bar. (If it is grayed
out, highlight the Sample Templates folder again, or right-click
the Sample Template folder and select Create from the shortcut
menu that appears.) (Figure A.12)
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Figure A.12
Sample Template window
The Create Template window appears (Figure A.13).
Figure A.13
Create Template window
44. Enter the name of the template (for example, Sample_Temp).
Click OK.
The sample template attributes window appears (Figure A.14).
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Figure A.14
Sample Template Attributes window
45. Double-click in the Name field to get a blinking cursor.
46. Enter Additional Comments in the Name field.
47. Select String in the Type field.
48. Select No in the Required field.
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Figure A.15
Attributes and Values Entered
49. Click Apply.
The Experiment and Sample templates are created and appear in
the left hand pane (Figure A.16).
You must select the Experiment or Sample template folder to see
the list of available templates.
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Experiment
and sample
templates
added
Figure A.16
Experiment and Sample Templates Added
ROLES TAB
The roles tab is only available when using GCOS Manager with a
registered GCOS server.
50. Click the Roles tab.
The Roles tab is used to set up security for the end-users.
Therefore, the functions of the Roles tab are solely for the use of the
system administrator and the tab only appears for users who have
been granted the Maintain Roles privilege.
51. Click GCOS Server Administrator from the left hand pane
under the name of the GCOS server.
The function of the GCOS Server Administrator is displayed. All
privileges are granted for the administrator (Figure A.17).
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Figure A.17
Administrator Privileges window
52. Click GCOS Server User from the left hand pane under the
GCOS server name.
The function of the GCOS Server User is displayed.
By default, all privileges are granted for the User except for the last
five privileges (Figure A.18).
Figure A.18
Default User Privileges
53. Under the GCOSServer3 database, expand the GCOS Server
Administrator group and GCOS Server User group.
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The domain name\Global Group appears and displays the group
members (Figure A.19).
Figure A.19
Roles Tab window
54. Click the right hand pane to expand the domain and the list of
Global Groups.
55. Expand the GCOS Server Global Group.
56. Drag a specific user to the GCOS Server User or GCOS Server
Administrator group.
This allows individual users or Global Groups access to certain
functions on the GCOS server.
57. Click any existing role in the left pane.
58. In the Create Role dialog box, type a name for a new role.
59. Click OK.
The new role appears in the left pane under the server.
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Figure A.20
Roles Tab window
EVENT VIEWER AND SERVER TASKS
60. To display the Event Viewer for the GCOS server, select Tools →
Server Event Viewer from the menu bar.
The Event Viewer for the GCOS server is displayed
(Figure A.21).
You can view the System, Security and Application Log.
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61. Close the Event Viewer.
62. To view the Server Tasks, select Tools → Server Tasks from the
menu bar.
This monitors and displays the status of any published data and
grows as more data are published.
Figure A.21
Server Tasks window
The task list is populated after experiment data are published.
GCOS 1.4 Testing
PREPARING AND SCANNING AN EXPERIMENT
63. Select File → New Experiment from the menu bar or click the
Experiments button
.
The Sample and Experiments window is displayed
(Figure A.22).
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Figure A.22
Sample and Experiments window
64. Enter the following information for Experiment 1 (Figure A.23):
- Sample Name: MySample
- Sample Type: SampleType
- Project: SampleProject
- Experiment Name: TestExp
- Probe Array Type: Hu6800
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Figure A.23
Experiment 1 input
65. Save the experiment information by selecting
File → Save from the menu bar or click the Save button
.
66. Enter the following information for Experiment 2 (Figure A.24):
- Sample Name: MySample
- Sample Type: SampleType
- Project: SampleProject
- Experiment Name: TestExp_2
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- ProbeArray Type: Hu6800
67. Select the Analysis Set (MySet) that was created in GCOS
Manager. (Only analysis sets for the same probe array type appear.)
68. Select the Publish Database (MyPub) that was created in GCOS
Manager.
69. Select Publish Intensities.
Figure A.24
Experiment 2 input
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70. Save the experiment information by selecting
File → Save from the menu bar or click the Save button
497
.
71. A dialog box appears prompting for the publish database
password. Enter the password and click Login.
72. From the Sample Template drop-down list, select
Sample_Temp.
73. From the Experiment Template drop-down list, select
Exp_Temp.
74. Enter the following information for Experiment 3 (Figure A.25):
- Sample Name: MySample
- Sample Type: SampleType
- Project: SampleProject
- More Comments: This is a test.
- Experiment Name: TestExp_3
- ProbeArray Type: Hu6800
- Comments: Additional comments
75. Set Analysis Set and Publish Database to [No analysis] and [No
publish] respectively.
76. De-select Publish intensities.
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Figure A.25
Experiment 3 input
77. Save the experimental information by selecting
File → Save from the menu bar or click the Save button
.
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HYBRIDIZING AN EXPERIMENT
78. To hybridize an experiment, select Run → Fluidics from the
menu bar or click Instrument Control in the shortcut bar and
click the Fluidics button
.
79. Select Module 1 (Figure A.26).
Figure A.26
Fluidics Station window
80. In the Experiment drop-down box, select TestExp.
81. In the Protocol drop-down box, select the protocol to run the
experiment on. (Select the appropriate fluidics protocol for the
probe array type.) (Figure A.27).
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Figure A.27
Select Protocol
82. Click Run.
The Fluidics Station window displays the Current Stage of the
hybridization (Figure A.28). This takes a few minutes.
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Figure A.28
Hybridizing experiment
Figure A.29
Hybridization complete
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Hybridizing done is displayed when complete (Figure A.29). The
experiment is ready to be scanned.
83. Click each module to verify that the hybridization is complete.
84. Click Close to exit the Fluidics station window.
85. For TestExp_2, select the GeneChip Software
shortcut bar and click the Workflow Monitor icon
Figure A.30
Workflow monitor window
.
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86. If you want to skip the hybridization step and place the
experiment in scan status, right-click TestExp_2 and select
Advance to Scan from the shortcut menu that appears
(Figure A.30).
SCANNING AN EXPERIMENT
87. To scan an experiment, select Run → Start Scanner from the
menu bar, or click Instrument Control in the Instrument
Control shortcut bar and then the Start Scanner button
.
Figure A.31
Scanner dialog box
88. Select TestExp from the Experiment Name drop-down list.
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Figure A.32
Scanner dialog box, TestExp selected for scan
89. Click Start to begin scanning the chip.
Figure A.33
Scanner prompt
Scanning a chip through one scan takes approximately 5 minutes.
Only one chip can be scanned at a time.
90. Load the chip into the scanner.
After the scan is completed, GCOS generates a .cel.
91. Scan the second experiment: from the menu bar select Run →
Start Scanner or click the Instrument control shortcut bar and
click the Start Scanner button
.
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92. From the Experiment Name drop-down list, select TestExp_2.
93. Click Start to begin scanning the probe array.
After the scan is completed, this experiment has the program
automatically create the .cel and the .chp and publishes them into
the MyPub database. This is done because Analysis Set and
Publish Database fields were selected during the experiment
setup.
94. Do not scan TestExp_3.
RUNNING AN ANALYSIS
95. To generate a .chp, select the TestExp.CEL.
96. Right-click TestExp.CEL file and select Analyze (Figure A.34).
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Figure A.34
Analyze Experiment window
The status log displays that it is running an analysis for the file.
For example, Running analysis for
\\<servername>\GeneChip\Affy_Data\Data\TestExp.CHP (Figure
A.35).
Figure A.35
Status log
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97. The status log displays when the analysis is completed (i.e.
Analysis completed for
\\<servername>\GeneChip\Affy_Data\Data\TestExp.CHP). The
.chp file is displayed.
If an error message is displayed, make a note of the error message
and follow the suggestions in the error message. If problems
persist, see Appendix K, Troubleshooting, on page 715.
Figure A.36
Analysis output file (.chp) displayed
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PUBLISHING
98. To Publish an experiment, select Run → Publish from the menu
bar or click the Publish button in the GeneChip Software
shortcut bar .
The Publish window appears (Figure A.37).
Figure A.37
Publish window
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99. To add data to be published, select Publish → Add Item from
the menu bar or click the Add button
in the publish window
area.
The Open window appears and displays experiments available for
publishing (Figure A.38).
Figure A.38
Open window
100.Highlight the TestExp experiment and click OK.
101.To publish the cell intensity data, select Publish → Options →
Publish Intensities from the menu bar.
The Publish Database Login window appears.
102.Enter the password for the publish database and click Login.
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Publish intensities: YES
Figure A.39
Publish window with intensities selected
103.To begin the publishing process, select Publish → Publish from
the menu bar or click the Publish button
in the publish
window.
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Figure A.40
Publish status window
104.The task window shows the status of the publishing process.
Each task contains items that are in a particular task.
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Figure A.41
Publish task item window
RUNNING REPORTS
105.To configure the report settings, select Tools → Report
Settings → Expression Report from the menu bar, or click the
Report
Settings in the shortcut bar and click Expression Report .
The Expression Report window appears (Figure A.42).
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Figure A.42
Expression Report window
106.Select File → Report from the menu bar and select the .chp to
generate the report; or
Right-click a .chp in the data file tree, and select Report (use the
TestExp.CHP file).
SAMPLE HISTORY
107.To view the sample history window (Figure A.43), select Run →
Sample History from the menu bar; or
Click the Sample History button
in the shortcut bar.
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Figure A.43
Sample history window
108.Click a sample.
The list of files pertaining to the sample appears in the right hand
pane (Figure A.44).
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Figure A.44
Sample history window, selected file
109.To view more history information, click the EXP icon
and
information in the results window is displayed (Figure A.25).
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Figure A.45
History for the selected file
110.To view history information, click the .dat, .cel, or .chp, click the
file.
The history information is displayed in the bottom windowpane.
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WORKFLOW MONITOR
111.To view the workflow monitor, select Run → Workflow
Monitor from the menu bar; or
Click the Workflow Monitor icon
in the GeneChip Software
shortcut bar.
112.To filter information, select Tools → Filters… from the menu
bar to display the Filters window.
113.Information can be filtered on the following items:
- Assay Type
- Sample Name
- Experiment
- Sample Project
- Probe Array Type
- Sample Type
- User
- Date
114.Click OK after any filter selections have been made.
115.The Workflow Monitor shows the current stage of the
experiment. The experiment could be in the following stage
status:
- Experiment Setup
- Hybridization
- Scan
- Grid Alignment
- Cell Intensity Analysis
- Probe Array Analysis
116.Click the bottom tabs to see the stage where experiments
currently stand.
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Data Mining Tool 3.1 Testing
1. Is your GCOS server using a SQL Server or Oracle® database?
2. If using SQL Server, go to step 5. If using Oracle, go to step 3.
3. If using Oracle, verify that Oracle client utilities are installed.
4. Verify that the alias or aliases (if using a remote GCOS server) are
created.
When you open the Data Mining Tool (DMT) for the first time a
message appears stating “Unable to Determine Publish Database
Name”. Click OK. This message appears because a publish
database has not yet been registered.
5. Start Data Mining Tool (Start → Programs → Affymetrix →
Data Mining Tool).
6. Select Edit → Register Database from the menu bar.
The Register Database dialog box appears (Figure A.46).
Figure A.46
Register Database dialog box, publish database on GCOS server
(Oracle® dialog box, top; Microsoft® SQL Server dialog box, bottom)
7. If using an Oracle database, go to Step 8. If using a Microsoft®
SQL Server database go to Step 10.
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8. Enter the server’s alias name in the Oracle Alias box.
9. Enter the Publish Database name, then go to Step 12.
10. Enter the Server Name, then click List Databases to display the
publish databases for the server in the Publish Database dropdown list.
11. Select a database from the Publish Database drop-down list.
12. Click Register.
DMT prompts for the Publish Database Password.
13. Enter the Password and click Login.
The database is available to DMT.
14. Select Edit → Select Data Source from the menu bar.
15. Select the Oracle Publish DSN (MyPub, or the name of the DSN
created).
16. Select Data → New → Expression Data Mining Tool from the
menu bar.
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Figure A.47
Data Mining Tool window
17. Verify that the data published appears in the DMT window.
18. From the menu bar, select Query → Run Query to execute query
or click the Query icon .
The query results window is displayed (Figure A.48).
appendix A | Client Testing
Figure A.48
Query Results window
19. Pivot the query results data by selecting Query → Run Pivot
from the menu bar or click the Pivot button .
Figure A.49
Pivot running
20. Graph the results by selecting Graph → Scatter...
from the menu bar or click the Scatter Graph button
.
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Figure A.50
Scatter Graph dialog box
21. Move the analysis files to the X-Axis and the Y-Axis. Click OK
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523
Figure A.51
Scatter Graph
GCOS Manager Additional Testing
This additional testing allows the system administrator to delete,
archive, unarchive, export or take ownership of data.
22. Start GCOS Manager 1.4
(Start → Programs → Affymetrix → GCOS Manager).
23. Expand the Samples list.
24. Expand the Expression Sample list.
EXPORT AN EXPERIMENT
25. Select Tools → File Path from the menu bar, or
click the File Path button .
26. Select a path location to export the files to (for example, x:\temp).
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27. Click the sample named MySample and select Process → File
View.
28. In the right hand pane, select TestExp and right-click to select
Export, or go to the menu bar and select Process → Export after
selecting the TestExp (Figure A.52).
Figure A.52
Export window
The task window displays the export process. It exports the .dat,
.cel, and .chp (Figure A.53).
Figure A.53
Status window
29. Once completed, the status returns to Available. If it fails, the
status returns ‘Failed.’
30. To view the error, double-click the Export icon in the Local Task
pane .
A text file appears. View the error message and try to resolve it. Try
exporting again.
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525
ARCHIVE AND UNARCHIVE
31. Click the Process Tab.
32. Expand the TestExp list in the right hand pane.
33. Select the TestExp.CEL file.
34. Right-click and select Archive (Figure A.54), or select Process
→ Archive from the menu bar.
Figure A.54
Archive window
The Select Archive Path Location window appears (Figure A.55).
Figure A.55
Archive Path Location window
35. Select the path location to archive the files to (for example,
c:\temp). Click OK.
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The archive process begins. All files are archived from the parent
down. If there are any files below, it archives them as well. In this
example, the .cel and .chp are archived.
The archive process is completed when the status is Available.
Figure A.56
Status window
36. Click MySample in the Samples list and select Process →
Refresh from the menu bar.
37. Expand TestExp in the right hand pane.
The files are archived and are displayed in gray.
38. To unarchive, right-click the archived file and select Unarchive;
or
Click the archived file and select Process → Unarchive from the
menu bar.
The Unarchive process begins.
PUBLISH DATABASE DATA DELETION
39. To delete files from the Publish database, select the Publish tab.
40. Expand the Probe Array Type list.
A list of probe array types is displayed of published experiments.
41. Click Hu6800.
The published experiments is displayed.
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42. Click TestExp.
This expands the list to display the .cel and .chp files
(Figure A.57).
Figure A.57
Publish Tab
43. Select the TestExp.CHP file (the last file), right-click and select
delete or select Publish → Delete from the menu bar.
The confirmation message to delete appears (Figure A.58).
Figure A.58
Confirmation to delete selected Publish data
44. Click Yes.
A message appears informing that the file is being deleted. The
deleted .chp is removed from the data tree.
45. If the experiment remains in the process database, the data can be
republished.
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PROCESS DATABASE DATA DELETION
46. To delete data from the process database, select the Process tab.
47. Expand the Expression Samples list.
48. Expand MySample.
49. Right-click TestExp and select Delete from the shortcut menu
that appears; or
Click TestExp and select Process → Delete from the menu bar.
A confirmation window appears (Figure A.59).
Figure A.59
Confirmation to delete specific experiment selected
50. Click Yes.
After deletion, the experiment is removed from the list.
51. Client testing completed.
Appendix
B
Installing Data Mining Tool 3.1
Appendix
B
531
Installing Data Mining Tool 3.1
The installation of Data Mining Tool 3.1 does not remove any
previous versions of Data Mining Tool. If the DMT is installed in the
same directory, it overwrites the previous versions’ files.
Data Mining Tool 3.1
This section guides you through the installation of Data Mining Tool
3.1. Listed below is an overview of the steps needed to complete the
installation:
MICROSOFT® SQL SERVER GCOS SERVER USERS
Obtain the name of the GCOS server from your IT personnel if not
known (this is needed during installation).
2. Install Data Mining Tool 3.1.
1.
ORACLE® GCOS SERVER USERS
Install Oracle® Client Utilities on the workstation (Oracle Client
Utilities must be the same version installed on the GCOS server).
2. Install SQL* Loader (for better performance).
3. Create an Oracle® Alias. For more information, refer to the
Affymetrix® GeneChip® Operating Software Server Installation and
Administration Guide.
4. Install Data Mining Tool 3.1.
The following are detailed installation instructions for installing
DMT.
1.
The screen captures depicted in this section may not exactly match
the windows displayed on your screen.
You must be logged in as administrator to install the DMT 3.1
software.
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To install DMT:
Log in as an administrator.
2. Insert the Affymetrix® DMT 3.1 CD-ROM.
3. If the autorun feature does not start the program:
1.
Click Start → Run.
B. Type <cd drive letter>:\setup.exe.
C. Click OK.
The Affymetrix Software Setup window appears, followed by the
Welcome window (Figure B.1).
A.
Figure B.1
Welcome window
Click Next.
5. Several consecutive Software License Agreement windows appear.
Review the contents in each and click Yes to accept the terms of
the agreement.
The Customer Information window appears (Figure B.2).
4.
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533
Figure B.2
Customer Information window
6.
Enter your Name, Company and Serial Number.
The serial number is located on the Affymetrix® Software Product
Registration card.
If you do not have a serial number, contact Affymetrix Technical
Support. If you are upgrading from a previous version, the Serial
Number field populates automatically.
7.
Click Next.
The Choose Destination Location window appears (Figure B.3).
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Figure B.3
Choose Destination Location window
8.
Click Next.
The Select Database Compatibility window appears (Figure B.4).
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535
Figure B.4
Select Database Compatibility window
9.
Select the database that DMT will connect with.
- Affymetrix® GCOS Server - if connecting to a GCOS server
- Affymetrix® GCOS - if connecting to the local MSDE
database
10. Click
Next.
The Select Database Type window appears (Figure B.5).
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Figure B.5
Select Database Type window
11. Select the database used on the GCOS server, either SQL Server or
Oracle.
If you do not know the type of database you are using with the
GCOS server, please contact your IT personnel or DBA.
12. Click Next.
The Enter Information window appears (Figure B.6).
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537
Figure B.6
Enter Information windows for the Microsoft® SQL Server database (left) or the Oracle® database (right)
13. In
the Enter Information window complete one of the following;
- If SQL Server is selected, enter the SQL Server Name (usually
the name of the GCOS server).
- If Oracle® is selected, enter the Oracle Alias Name.
14. Click
Next.
The Start Copying Files window appears.
15. In the Start Copying Files window, verify the information and
click Next.
Program files are copied and the system configures the registry.
Database connectivity is verified.
For Oracle® systems: If a warning message regarding SQL Loader
appears, continue the DMT install until complete. Then, install SQL
Loader (part of Oracle) for better DMT performance. After SQL
Loader is installed, re-install DMT.
The Setup Complete window appears.
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16. Select
Yes, I want to restart my computer now and click
Finish.
Appendix
C
GCOS Instrument Installation
Appendix
C
541
GCOS Instrument Installation
The instrument installation needs to be done only on an instrument
system.
The instrument installation needs to be run if there has been a change
to any of the drivers, otherwise upgrading the software to GCOS is the
only installation upgrade required.
The instrument installation is for Microsoft® Windows® 2000
Workstation only.
This appendix contains the following sections:
• The Affymetrix® Scanner 3000 with Fluidics Station Installation (see
below)
• Fluidics Station Installation (only) (see page 548)
• GeneChip® Scanner 3000 Installation (only) (see page 553)
For information on installing and using the GeneChip Scanner 3000
with Autoloader, see Appendix L, Using the GeneChip® AutoLoader, on
page 731.
The Affymetrix® Scanner 3000 with Fluidics Station
Installation
Follow this section if you have the GeneChip® Scanner 3000.
When you install the fluidics station software, confirm the presence of
the correct Sealevel card.
If you cannot confirm the presence of a Sealevel card, contact
Affymetrix technical support.
1.
On an instrument workstation that will be controlling fluidics
stations, there must be a Sealevel card for communication between
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the workstation and the fluidics stations. Review Figure C.1 to
confirm that a Sealevel card is installed in your system.
A single 25
pin connector
25 pin cable
adaptor
Figure C.1
Confirming the Sealevel card setup: note the 25 pin connector and the 25 pin
cable adaptor
Launch Microsoft® Windows® 2000 Explorer.
3. Browse to the Instrument CD.
4. Double-click setup.exe within the Instrument CD.
The Welcome window appears.
2.
Click Next.
6. Several consecutive Software License Agreement windows
appear. Click Yes in each window to accept the terms of the
agreement.
The Choose Destination Location window appears (Figure C.2).
5.
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543
Figure C.2
Choose Destination Location window
7.
Click Browse and select the Destination to install the instrument
driver (select the same location where you installed GCOS).
8.
Click Next.
The Select Components window appears (Figure C.3).
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Figure C.3
Select both the Scanner Files and Fluidics Station and Sealevel card files
9.
Select both the Affymetrix Scanner Files option and the
Fluidics Station Files option (Figure C.3). Highlight the
Affymetrix Scanner Files option and click Change... to select
the type of scanner.
The following dialog box opens and displays the choice of scanners,
Affymetrix® GCS 3000 Scanner and GeneArray® 2500 Scanner
(Figure C.4).
appendix C | GCOS Instrument Installation
545
Figure C.4
Select the Affymetrix scanner. Select one scanner but not both.
the Affymetrix® GCS 3000 Scanner and click Continue.
If you click Continue with both scanners selected, the software
will display the following message.
10. Select
11. Click
Next and enter the Port # for the COM serial port for the
Sealevel serial card. Enter 2 (Figure C.5).
If the workstation is the Dell GX110, select COM Port 3.
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Figure C.5
Select the Port Number for the Sealevel card.
12. Click
Next.
The Start Copying Files window appears (Figure C.6).
This is a summary of the information selected.
appendix C | GCOS Instrument Installation
547
Figure C.6
Start Copying Files Window
13. Review
the information and click Next to continue.
Program files and device drivers are copied to your system, and the
Setup Complete window then appears (Figure C.7).
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Figure C.7
Install Complete window
14. Click
Finish.
Fluidics Station Installation (only)
When you install the fluidics station software, confirm the presence of
the correct Sealevel card.
If you cannot confirm the presence of a Sealevel card, contact
Affymetrix technical support.
1.
On an instrument workstation that will be controlling fluidics
stations, there must be a Sealevel card for communication between
the workstation and the fluidics stations. Review Figure C.8 to
confirm that a Sealevel card is installed in your system.
appendix C | GCOS Instrument Installation
549
A single 25
pin connector
25 pin cable
adaptor
Figure C.8
Confirming the Sealevel card setup: note the 25 pin connector and the 25 pin
cable adaptor
2.
3.
4.
5.
6.
Launch Microsoft® Windows® 2000 Explorer.
Browse to the Instrument CD.
Double-click setup.exe within the Instrument CD.
The Welcome window appears.
Click Next.
Several consecutive Software License Agreement windows
appear. Click Yes in each window to accept the terms of the
agreement.
The Choose Destination Location window appears (Figure C.9).
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Figure C.9
Choose Destination Location window
Click Browse and select the Destination to install the instrument
driver (select the same location where you installed Microarray
Suite).
8. Click Next.
The Select Components window appears (Figure C.10).
7.
appendix C | GCOS Instrument Installation
551
Figure C.10
Select only the Fluidic Station and Sealevel card files.
Select the Fluidics Station Files option (Figure C.10).
This should be the only option selected.
10. Click Next.
11. Enter the Port # for the COM serial port for the Sealevel serial card.
Enter 2 (Figure C.11).
9.
If the workstation is the GX110, GX260 or GX270, select COM Port
3.
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Figure C.11
Select the Port Number (Sealevel card only)
12. Click
Next.
The Start Copying Files window appears (Figure C.12).
This is a summary of the information that you selected.
Figure C.12
Start Copying Files Window
appendix C | GCOS Instrument Installation
553
13. Review
the information and click Next to continue.
Program files and device drivers are copied to your system, and the
Install Complete window appears (Figure C.13).
Figure C.13
Install Complete window
14. Click
Finish.
GeneChip® Scanner 3000 Installation (only)
The instrument installation is for Microsoft® Windows® 2000
Workstation only.
Launch Microsoft® Windows® 2000 Explorer.
2. Browse to the Instrument CD.
3. Double-click setup.exe within the Instrument CD.
The Welcome window appears.
4. Click Next.
1.
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Affymetrix® GeneChip® Operating Software User’s Guide
Several consecutive Software License Agreement windows
appear. Click Yes in each window to accept the terms of the
agreement.
The Choose Destination Location window appears (Figure C.14).
Figure C.14
Choose Destination Location window
Click Browse and select the Destination to install the instrument
driver (select the same location where you installed Microarray
Suite).
7. Click Next.
The Select Components window appears (Figure C.15).
6.
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555
Figure C.15
Select Affymetrix Scanner files only for scanner installation
8.
Select only the Affymetrix Scanner Files option. Highlight the
Affymetrix Scanner Files option and click Change... to select
the type of scanner.
The following dialog box opens and displays the choice of scanners,
Affymetrix or GeneArray® (Figure C.16).
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Figure C.16
Select the Affymetrix scanner. Select one scanner but not both.
9.
Select the Affymetrix Scanner files and click Continue.
If you click Continue with both scanners selected, the software
will display the following message.
10. Click
Next.
The Start Copying Files window appears (Figure C.17).
This is a summary of the information that you selected.
appendix C | GCOS Instrument Installation
Figure C.17
Start Copying Files Window
11. Review
the information and click Next to continue.
The Install Complete window appears (Figure C.18).
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Figure C.18
Install Complete window
12. Click
Finish.
Appendix
D
Using the GeneChip® Scanner 3000
Appendix
D
561
Using the GeneChip® Scanner 3000
Affymetrix has designed a new scanner expressly for scanning
GeneChip® probe arrays. The GeneChip® Scanner 3000 requires little
maintenance.
The instrument must be kept clean and free of dust. Dust buildup can
degrade performance. Wipe the exterior surfaces clean using a mild
dish detergent solution in water. Do not use ammonia based cleaners
or organic solvents, such as alcohol or acetone, to clean the system
because they may damage the exterior surfaces.
Figure D.1
The Affymetrix® GeneChip® Scanner 3000
Do not remove the cover of the scanner. Use the scanner only as
instructed in this User Guide. Do not attempt to service the
instrument.
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This appendix contains the following sections:
• Introduction (see below)
• Safe Operation (see page 564)
• Connections and Indicator Lights (see page 569)
• Using the Barcode Reader (see page 573)
• Scanner 3000 Specifications (see page 576)
• Troubleshooting (see page 577)
• CE Mark Declaration of Conformity (see page 583)
• Regulatory (see page 584)
Introduction
The Affymetrix® GeneChip® Scanner 3000 is a wide-field,
epifluorescent, near-confocal microscope. The scanner uses a 532 nm
solid-state laser to excite probe array fluorophores. This in turn
produces an emission wavelength appropriate for the probe array being
scanned, which is automatically specified in the scan parameters for
the selected probe array. As the surface of the probe array is scanned, a
photomultiplier tube collects and converts the fluorescent emissions
into an electrical signal. An analog-digital converter in the scanner
converts this signal into corresponding numeric values representative
of fluorescent intensities. These digital intensity values are collected
from discrete areas on the array surface and are stored on the computer
workstation as pixels that comprise the image data file (the .dat file).
For more information on image data, see Chapter 9, Working with
Images, on page 141.Affymetrix’ patented Flying Objective™
technology represents a radical departure from conventional laser
scanners. The optical system comprises a scan arm that rapidly
oscillates from side to side scanning the entire width of the probe array
in a continuous arc while the probe array is advanced in front of the
objective. The acquired image of the array is returned to the computer
software as a set of arcs. The software then geometrically corrects these
arcs to form a linear image of the array (Figure D.2).
appendix D | Using the GeneChip® Scanner 3000
563
Figure D.2
Schematic of the scanner design
The laser source excites the hybridized fluorophores and the
photomultiplier system simultaneously captures the resulting
fluorescent intensities. The optical components direct the fluorescent
beam back through the objective lens, through a dichroic mirror and
to the PMT. An analog-digital converter transforms the PMT output
into 65536 levels of intensity. Each level of intensity is stored in the
software as a 16 bit number (216=65536).
The scanner is equipped with an IEC 320 compliant power entry
module located at the rear of scanner (Figure D.3).
The scanner is equipped with an RJ-45 interface connector compatible
with 10/100 Base T Ethernet for communications with the host
workstation.
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The GCOS application controls the scanner. The scan process times for
each type of GeneChip® probe array are outlined in the next table.
Affymetrix measures the process time from the “Start Scan” command
to the return of the cartridge to the instrument entrance port along
with the display of the completed scan image on the workstation
monitor.
Probe Array Type
Process Time (typical)
49
5min 15sec
64
4min 30sec
100
3min 30sec
169
3min 30sec
400
2min 45sec
After the scanner has completed a scan, GCOS displays a picture of the
image in the image window. The software displays the fluorescent
intensity values from each pixel within the probe array feature in a
grayscale or pseudocolor mode and superimposes a grid on the image
to delineate the probe cells.
GCOS analyzes the image and derives a single intensity value for each
probe cell on an array. This data is automatically generated and saved
to the cell intensity file. See Chapter 9, Working with Images, on
page 141.
The file containing the completed analysis of the probe .cel files to
provide the appropriate present, absent or marginal calls.
Safe Operation
To ensure safe operation of the GeneChip® Scanner 3000:
• Read this section and Scanning a Probe Array–GeneChip® Scanner
3000, on page 121 completely before operating the instrument.
appendix D | Using the GeneChip® Scanner 3000
565
• Do not attempt to service this instrument. Any attempt at
unauthorized service may damage the instrument and/or void the
warranty.
• The instrument weight is approximately 63 pounds (28.6 Kg).
Do not place it on an unstable cart, stand, or table. Failure to
properly support the instrument may cause serious damage or
injury and may void the warranty.
Heavy object. Two people are required to lift the scanner.
• The instrument must be surrounded by adequate airspace. Slots
and openings in the instrument and the electronics compartment
covers are for ventilation. Do not block or cover them.
• Never push an object into the instrument ventilation slots;
equipment damage or injury may result. Do not set liquids on top
of the instrument.
• The instrument has an AC receptacle with a safety ground
appropriate for the country of destination. The plug is designed to
connect only to a 3-prong ground receptacle. This safety feature
should not be compromised in any way. If the instrument AC
plug does not mate with the available power source receptacle,
consult a licensed electrician to install one that does.
When to Contact Affymetrix
Under any of the following conditions, unplug the instrument from
the power source and contact technical Support:
• When the power cord is damaged or frayed.
• If any liquid has been spilled into the instrument.
• If the instrument has been penetrated by water.
• If, after service or calibration, the instrument does not perform in
accordance with the capabilities stated in the specifications.
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• If the instrument has been dropped or otherwise damaged.
If the instrument must be returned for repair, call Affymetrix®
Technical Support.
Do not remove the cover of the scanner. Use the scanner only as
instructed in this User Guide. Do not attempt to service the
instrument. Only qualified service technicians can open and service
the scanner. There are no customer serviceable parts. Removing
the case exposes the customer to laser and electrical shock hazards.
You can learn more about safety in the following sections:
• Laser Safety (see below)
• Electrical Safety (see page 567)
LASER SAFETY
The laser is equipped with an automatic shutter that inhibits its
output beam and ensures safe operation under conditions encountered
in normal operation. The instrument covers, probe array cartridge
access port, and protective shutters ensure that during instrument
operation no directed or stray laser light leaves the instrument.
The GeneChip scanner 3000 is a Class I laser product when the laser
is enclosed in scanner case. The laser itself is a Class IIIB laser
product.
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567
DANGER
Laser radiation when open.
Avoid direct exposure to beam.
The lasers can cause serious injury if
the instrument is not operated in
accordance with instructions in this
user guide.
CAUTION
Use laser safety glasses when
servicing
DO NOT STARE INTO BEAM.
The green laser is a 532nm solid-state laser. This is a Class IIIb laser
and has visible outputs greater than 5mw but no more than 500mw.
It must never be operated in an exposed manner. Any object in the
direct path of the laser beam may be damaged. Eyes and skin can be
seriously damaged by direct exposure to, specular reflections from, or
diffuse reflections from this laser. If improperly used, a laser of this
type can cause fires. When used according to the instructions in this
manual and when all covers are in place, the GeneChip® Scanner 3000
is classified as a Class I Laser Device per 21 CFR 1040.
Always take note of laser safety labels; they indicate areas where
exposure to laser beams may be hazardous.
ELECTRICAL SAFETY
The scanner will automatically handle any input voltage from 100 to
240 VAC nominal, 50 to 60 Hz
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The scanner’s power supply will autodetect the input voltage
source and configure itself.
CAUTION
CAUTION
The power supply cord is used as the main disconnect device. Ensure
that the socket outlet is located and installed near the equipment and
is easily accessible.
ATTENTION
Le cordon d’alimentation est utilisé comme interrupteur general. La
prise de courant doit être située ou installée a proximité du materiel et
être facile d’accés.
ACHTUNG
Zur sicheren Trennung des Gerätes vom Netz ist der Netzstecker zu
ziehen. Vergewissern Sie sich, daß die Steckdose leicht zugänglich ist.
Maintenance
The GeneChip® Scanner 3000 requires little maintenance.
The instrument must be kept clean and free of dust. Dust buildup can
degrade performance. Wipe the exterior surfaces clean using a mild
dish detergent solution in water. Do not use ammonia based cleaners
or organic solvents, such as alcohol or acetone, to clean the system
because they may damage the exterior surfaces.
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569
Connections and Indicator Lights
The GeneChip® Scanner 3000 has the following connections on the
back of the unit (Figure D.3):
• AC power connection
• Ethernet connection
If you must move the scanner, disconnect all cables first.
You can learn more about the connections and lights in:
• Connecting the Scanner (see below)
• Indicator Lights and On/Off Button (see page 570)
CONNECTING THE SCANNER
Connect the 3-pronged electric power plug to the workstation.
2. Connect the dedicated Ethernet cable from the scanner to the
Ethernet port that is designated on the workstation. The port is
located near the bottom of the workstation.
3. You can connect your company’s network cable to the indicated
port near the center of the workstation.
When you start GCOS, the software will make the proper
communication connections.
1.
Do not confuse your company’s network connections with the
dedicated Ethernet port of the scanner-workstation. The proper
scanner connection is located near the bottom of the workstation.
This 10/100 Base T Ethernet communications port is dedicated to
the scanner-workstation interface. You cannot connect the scanner
to your company’s Ethernet communications network.
You can, however, connect the workstation’s second Ethernet port
to the your company’s Ethernet network.
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Figure D.3
Scanner Connections- left: rear of scanner -right: rear of computer
The reset button is the scanner’s circuit breaker. The breaker switch
will be tripped whenever the scanner experiences an electrical fault
condition. Press to reset. If you cannot reset this switch, contact
Affymetrix technical support.
INDICATOR LIGHTS AND ON/OFF BUTTON
The front panel has the following button and indicators (Figure D.4).
appendix D | Using the GeneChip® Scanner 3000
571
Blue
Indicator
Light
Yellow light
Green light
I/O (on/off)
button
Figure D.4
Scanner indicator lights and on/off (I/O) button
I/O (on/off) button in the center.
2. Blue indicator light, running vertical at front center, indicates that
the scanner is on.
3. Green and yellow light both on indicate scanner boot up in
progress.
1.
4.
Yellow light
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On = Idle, laser is warming up (laser not ready, green off)
B. Off = System ready, no errors (Green on)
C. Flashing = Error
5. Green light
A.
A.
On = System is ready to scan (yellow off)
B.
Flashing = Scan in progress
Summary of Indicator Lights
The table below summarizes the light conditions and their meaning.
Table D.1
Indicator lights
Condition
Green
Light
Yellow
Light
Blue
Indicator
Light
Meaning
Initial boot up
Off
Off
On
Initial power up; embedded
PC takes control
Scanner boot
up
On
On
On
Embedded PC takes control
of scanner boot up
Laser warm up
Off
On
On
Software enabled and laser
is warming up
System ready
On
Off
On
User communication with
scanner enabled
Error
Off
Flashing
On
Fatal error, reboot scanner
and software
Scanning
enabled
Flashing
Off
On
Scanning in progress
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573
During the initial power up (CPU boot up), both the green and
yellow lights will be off.
During the scanner boot up, both the green and yellow lights will
be on.
Using the Barcode Reader
If your scanner is equipped with a barcode reader, follow this section
for instructions on its use.
1.
Open the GCOS software to the Experiment Information window
and place the cursor in the barcode reference field of the GCOS
Experiment Information window (Figure D.5).
You should open a new experiment and place the cursor into the
barcode field before triggering the reader. Otherwise, the barcode
will be misinterpreted as some other kind of input. You are required
to open a new experiment for each barcode and must enter certain
other information before the experiment can be saved. See
Table L.4 on page 759 for a summary of information that you can
enter in the Experiment Information Window.
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Figure D.5
Experiment Information Window with cursor in the barcode field
2.
Hold a GeneChip probe array cartridge in front of the barcode
reader and squeeze the trigger for approximately four seconds until
you hear a beep (Figure D.6).
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575
Figure D.6
Reading the cartridge barcode
3.
The reader reads and sends the barcode to the GCOS Experiment
Information window, Barcode field (Figure D.7).
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Figure D.7
Experiment Information Window with barcode
After the software adds the barcode, save the experiment.
5. Repeat steps 1 to 4 until all of the probe array cartridges have been
read.
4.
Scanner 3000 Specifications
Item
Weight
Dimensions
Parameter
Value
Shipping
approx 78 pounds (35.4
Kg)
Free-standing
63 pounds (28.6 Kg)
Width
~13.25 in.
Depth
~27.5 in.
Height
~18.25 in.
appendix D | Using the GeneChip® Scanner 3000
Item
Parameter
577
Value
Power
Voltage
Current
Line Frequency
100 - 240 V ~
4-2A
50 - 60 Hz
Working Environment
Temperature
59°F-85°F (15°C-30°C)
Humidity
10-90% Non-condensing
Clearance
2 in. (5 cm) on side, back
and top
Pollution Degree
2
Installation Category
II
Altitude
<2000m
Electrical Supply
Provide voltage, frequency or power rating per unit
label
Main Supply Voltage
Fluctuations
Are not to exceed ±10% of the nominal supply
voltage
If you use the scanner in a manner not specified in this user guide,
you may impair the protection provided by the equipment.
Troubleshooting
Problem
No image when
scanning
Intermittent problems
scanning
Possible Cause
Corrective Action
Power off or cable loose
Check all connections
and power.
Loss of laser power
Contact technical
support.
Loose cable
Check all rear
connections.
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Problem
Scanner fails with probe
array inside
Possible Cause
Power failure
Corrective Action
Manually extract probe
array. Check all
connections to scanner.
Turn scanner on, restart
software.
You can learn more about troubleshooting in:
• Issues Relating to the Scanner’s Operation (see below)
• Manually Removing a Lodged Probe Array Cartridge (see page 579)
ISSUES RELATING TO THE SCANNER’S OPERATION
The GeneChip® Scanner 3000 is a new type of scanner. In using the
scanner you may encounter some issues, or problems, that may require
your intervention. Below is a list of these issues.
Issue
Explanation
If communications are
interrupted during a scan (by
a faulty cable connection or
power being lost at the
scanner, for example)
GCOS will properly note the failure and present a message “Cannot connect
to Scanner.” However, there are two issues to note. First, GCOS will report
such a failure only after a network time-out of about 30 seconds. Second,
rarely, if communications have been lost, GCOS and the Scanner may not
be able to automatically restore communications once the problem is
rectified, and both may become unresponsive.
To restore proper operation, verify that the scanner is on, that
communication cables are properly connected, and close and restart
Microsoft® Windows® then restart GCOS. If the system remains
unresponsive, disconnect and reconnect power to the scanner, restart the
scanner normally, close and restart Microsoft® Windows® and GCOS.
Repeated attempts to send
If communications cannot be re-established, please follow the
commands (Start, Turn Laser recommendations of item 1
On, etc.) from GCOS to the
Scanner while GCOS is
reporting the scanner
“Offline” may result in GCOS
becoming unresponsive until
communications are restored
appendix D | Using the GeneChip® Scanner 3000
Issue
579
Explanation
If the Scanner experiences
multiple auto-focus failures,
the system may enter an
unresponsive state.
Follow the recommendations of item 1 to restore communications and
correct operation.
Laser warm-up lasts for ten
minutes, during which time
the “Turn Laser On” button
will remain unchanged and
GCOS will display the status
message “Warm-up”.
Simply note that this is normal operation.
Occasionally, when
Reducing the graphics acceleration parameter in Microsoft® Windows®
observing DAT images in
desktop Properties will eliminate this problem.
GCOS, the user may notice, at
specific zoom levels, that grid
lines do not properly appear.
If no chip is inserted and a
scan started.
The scanner will attempt go through the first parts of the auto-focus routine
and then report “Failed to find chrome border”.
The scanner should be in the park mode to eject the chip.
Auto focus will fail if salt
deposits accumulate on the
array.
Use Tough-Spots® to prevent leaks in the GeneChip® probe array. See the
quick reference card, p/n 08-0076.
MANUALLY REMOVING A LODGED PROBE ARRAY CARTRIDGE
In the event that a probe array becomes lodged in the chip transport
mechanism, follow the procedure outlined below.
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1.
2.
Turn off the scanner.
Insert a paper clip or
small Allen wrench
into the rescue hole on
top of the scanner and
press to partially lift
the cartridge loading
door.
3.
Using your fingers, gently lift the front edge of the door. As you lift the front edge, lift the back edge
approximately 1/4” to open the door straight up to expose the rescue screw in the front.
appendix D | Using the GeneChip® Scanner 3000
4.
5.
581
Using a standard (-)
screwdriver, turn the
rescue screw clockwise
to raise the chip transport mechanism.
Continue to turn the
screw until the probe
array cartridge
ascends sufficiently to
grab it.
Note that the screw is fine pitched and requires a number of turns. Stop if you encounter
screw resistance. Do not over torque.
582
6.
7.
8.
When the cartridge
has ascended sufficiently, remove it.
Rescrew the chip
transport mechanism
until it descends completely, or until you
encounter resistance.
Do not over torque.
Close the door.
Affymetrix® GeneChip® Operating Software User’s Guide
appendix D | Using the GeneChip® Scanner 3000
CE Mark Declaration of Conformity
We, Affymetrix, Inc.
4G Crosby Drive,
Bedford, Massachusetts
Declare under sole responsibility that the Affymetrix® GeneChip® Scanner 3000 conforms with the
relevant provisions of the following standards or other normative documents:
EU EMC Directive 89/336/EEC:
EN 61326:1998
Equipment for Measurement, Control and Laboratory Use, EMC
Requirements
EN 55011:1998
Industrial, scientific and medical (ISM) radio-frequency equipment Radio disturbance characteristics - Limits and methods of
measurement
EN 61000-3-2:2001
Limits for harmonic current emissions (equipment input current up to
and including 16 A per phase)
EN 61000-3-3:1995
Limitation of voltage changes, voltage fluctuations and flicker in
public low-voltage supply systems, for equipment with rated current
less than or equal to 16 A per phase and not subject to conditional
connection
EN 61000-4-2:1995
Electrostatic discharge immunity.
EN 61000-4-3:1995
Radiated, radio frequency, electromagnetic field immunity.
EN 61000-4-4:1988
Electrical fast transient/burst immunity.
EN 61000-4-5:1995
Surge immunity.
EN 61000-4-6:1996
Immunity to conducted disturbances induced by radio frequency
fields.
EN 61000-4-11:1994
Voltage dips, short interruptions, and voltage variations immunity.
EU Low Voltage Directive 73/23/EEC
EN 61010-1:2001
Safety requirements for electrical equipment for measurement,
control, and laboratory use -- Part 1: General requirements
EN 60825-1:1994+ A2:2001
Safety of laser products -- Part 1: Equipment classification,
requirements and user's guide
583
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Affymetrix® GeneChip® Operating Software User’s Guide
Regulatory
This device complies with Part 15, Subpart B, Class B of the FCC rules.
Operation is subject to the following two conditions: (1) This device
may not cause harmful interference, and (2) this device must accept
any interference received, including interference that may cause
undesirable operation.
This device complies with FDA performance standards for laser
products except for deviations pursuant to Laser Notice No. 50, dated
July 26, 2001.
Regulatory Agency
Certification
AL 02 12 39816 004
92AA
See CE Mark Declaration of Conformity, on page 583.
Compliant with directive 2002/96/IC (WEEE)
Class I Laser Device
21 CFR 1040.10 and 1040.11
For Research Use Only. Not for use in diagnostic procedures.
Appendix
E
Configuring the GCOS Services
Appendix
E
587
Configuring the GCOS Services
GCOS provides services that help you automate your data
management:
• GCOS Analysis Service performs cell intensity analyses.
If you are using GCOS with a networked GCOS Server, you can
run the Analysis Service on the workstation or the server.
• GCOS Transfer Service lets you automate the archiving of DAT
files.
The GCOS Transfer Service cannot be used when working with a
GCOS Server and when analysis is set to be done on the remote
server. Use GCOS Manager to archive the data.
This appendix describes:
• The requirements for using the Analysis and Transfer services (see
below)
• How to configure the GCOS Service settings (see page 589)
• How to select the GCOS Service options (see page 597)
• How to set the Start/Stop Service policies so that the services will
run (see page 601)
• How to set the Act as Part of the Operating System policies so
that the services will run (see page 612)
Requirements for Using the GCOS Services
In order to use the GCOS Analysis and Transfer services you will need
to:
• Have a valid domain user and password set up with the necessary
privileges (see Domain User Requirements, below).
• For analysis on the client: The service has to be configured on the
client to run as:
(i) a user in the GCOS administrator role on GCOS server.
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(ii) with privileges to Start/Stop services as part of the user's
local system policies, i.e., has the “Log on as service” privilege.
• For analysis on the server: The service has to be configured on the
GCOS Server.
The service has to be configured on the server to run as:
(i) a user in the GCOS administrator role on GCOS server.
(ii) with privileges to Start/Stop services as part of the user's local
system policies, i.e., has the “Log on as service” privilege.
• For archiving data to a Universal Naming Convention (UNC)
location, the transfer service has to be configured to run as a user
that has access to the UNC path.
By default, the installation sets the services to run under the local
system account. This default is suitable for access to local machine
resources only and will prevent the data transfer and analysis services
from accessing UNC paths and other network resources. On a GCOS
Server, the services should not be configured to run under the
SYSTEM account if file security has been turned ON or if the GCOS
client workstation has Windows XP Service Pack 2.
If a client workstation has Windows XP Service Pack2, then the
GCOS Services on the GCOS server should be configured to run as
an authenticated domain user. If the service runs under the local
SYSTEM account then, the GCOS client will fail to receive status
messages about completion of CEL file generation after completion
of the scan.
DOMAIN USER REQUIREMENTS
If you wish to allow the transfer and analysis service to access network
resources and/or GCOS Server resources, you need to supply a valid
domain user and password that meets the following requirements:
• Has privileges sufficient to access the network resources (shares,
folders, files), that all users on the machine will require
appendix E | Configuring the GCOS Services
589
• Has privileges sufficient to access the process database objects and
be a member of a role that will allow access for all users on the
machine, when the machine is acting as the client of a GCOS
Server
• Has privileges to Start/Stop services as part of the user's local
system policies.
• On a Windows 2000 client, the user should also be part of the
“Act as local operating system” policy. For more information, see
Setting the Act As Part of the Operating System Policy, on page 612.
A user who is in the 'Administrator' role on the server meets these
requirements.
Configuring the GCOS Service Settings
After you have set up the domain user with the necessary privileges
and policies, you need to set the GCOS Service settings.
The analysis and transfer service use the same settings. Any change
to one service is applied automatically to the other service.
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Start GCOS UI and
open Defaults dialog
box
Is Client
configured to work
with server?
Yes
Does user want
to analyze CEL on
local
workstation?
No
Go to the server
and change analysis
Svc settings
No
Yes
No
Run as
System
Does user want
to archive to UNC
path?
Yes
Enter a domain user
who has access to UNC
On the client
open dialog to
change Svc
settings
If archiving, enter a
domain user who has
access to UNC
Figure E.1
Flow chart for setting the GCOS Service Options
You can configure the settings for:
• A stand-alone workstation system (see below)
• A system configured to work with a GCOS Server (see page 593)
• A GCOS Server (see page 595)
Refer to the flow chart (Figure E.1) for an overview of the GCOS
services options.
appendix E | Configuring the GCOS Services
591
CONFIGURING THE GCOS SERVICE SETTINGS ON A STAND ALONE
SYSTEM (NO GCOS SERVER)
To set the GCOS Service Setting on a stand-alone workstation (i.e.,
GCOS Server name is empty in the Database tab of the Defaults dialog
box):
1.
Click the Defaults button
in the shortcut window;
Or select Tools → Defaults from the menu bar.
The Defaults dialog box opens (Figure E.2).
Figure E.2
Defaults dialog box, Analysis Settings tab
Click the Archive Settings or Analysis Settings tab of the dialog
box.
3. Click the GCOS Service Settings button
.
The GCOS Service Settings dialog box appears (Figure E.3).
2.
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Figure E.3
GCOS Service Settings dialog box
The dialog box has the following controls:
4.
Domain
Domain on the network to which the GCOS Server is
assigned.
User
The network user ID assigned to the user.
Password
User’s password.
Run As Local System
When this is selected, the service will run under the NT
SYSTEM account.
Apply
Applies the entered changes.
Cancel
Closes the dialog box without applying the changes.
Select Run As Local System to use the databases installed on the
workstation;
The service can run under the Microsoft® Windows® SYSTEM
account if archiving is OFF. If archiving is ON, the service must
be configured to run under the user credential that has access to the
UNC path where data is to be archived.
Select Run as Local System if you do not plan on auto-archiving
DAT files immediately after scan to a networked drive.
appendix E | Configuring the GCOS Services
5.
593
Click Apply.
The selected options are applied.
CONFIGURING THE GCOS SERVICE SETTINGS ON A CLIENT CONFIGURED
TO WORK WITH GCOS SERVER
To set the GCOS Service Settings on a client configured with GCOS
Server:
1.
Click the Defaults button
in the shortcut window or select
Tools → Defaults from the menu bar.
The Defaults dialog box opens (Figure E.4).
Figure E.4
Defaults dialog box, Analysis Settings tab
2.
Click the Archive Settings or Analysis Settings tab of the dialog
box.
3.
Click the GCOS Service Settings button
The GCOS Service Settings dialog box appears (Figure E.5).
.
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Figure E.5
GCOS Service Settings dialog box
The dialog box controls are described on The dialog box has the
following controls: (see page 592).
4. Select the Domain/User you wish to use from the drop-down list
and enter the password for that user.
The analysis /transfer service must be reconfigured to run as a user
who has admin rights on the local machine and is in the GCOS
Administrator's role on the GCOS Server. The list is populated
automatically with a list of users who have the above mentioned
rights.
For more information about the requirements for the User, see
Requirements for Using the GCOS Services, on page 587.
5.
Click Apply.
The selected options are applied.
If you see the following error message (Figure E.6):
appendix E | Configuring the GCOS Services
595
Figure E.6
Error message
Review the requirements for using the GCOS Services
(see page 587).
B. Change the Start/Stop Services policies and other settings on
your system as necessary (see page 601).
A.
CONFIGURING THE GCOS SERVICE SETTINGS ON A GCOS SERVER
After you have set up the domain user with the necessary privileges
and policies, you need to set the GCOS Service settings.
To set the GCOS Service Settings on the GCOS Server:
1.
Click the Microsoft® Windows® Start button
Settings → Control Panels.
The Control Panel window opens (Figure E.7).
, then select
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Figure E.7
Control Panel
2.
Double-click the GeneChip Analysis and Transfer Icon.
The GCOS Service Settings dialog box opens (Figure E.8).
Figure E.8
GCOS Service Settings dialog box
The dialog box controls are described on (see page 592).
appendix E | Configuring the GCOS Services
3.
597
Select the Domain/User you wish to use from the drop-down list
and enter the password for that user.
If file security is ON, the service has to run under a user who has
admin rights on the GCOS Server and is in the GCOS
Administrator's role on the GCOS Server.
The list is populated automatically with a list of users who have the
above mentioned rights.
For more information about the requirements for the User, see
Requirements for Using the GCOS Services, on page 587.
4.
Click Apply.
The selected options are applied.
Selecting the GCOS Services Options
After you have configured the GCOS Service settings, you can select
the GCOS options to:
• Perform CEL Intensity analyses on the workstation or GCOS
Server using the Analysis Service (see below).
• Archive the DAT files after scanning using the Transfer Service
(see page 599).
The GCOS Transfer Service cannot be used when working with a
GCOS Server and when analysis is set to be done on the remote
server. Use GCOS Manager to archive the data.
Any changes applied to the transfer service will be applied
automatically to the analysis service.
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CELL INTENSITY ANALYSIS OPTIONS
If you are using GCOS with the GCOS Server, you can perform the
analysis of DAT files to produce CEL files on the GCOS Server or the
instrument workstation using the GCOS Analysis Service.
You must have a domain user with the proper privileges and
policies set up to use the cell intensity analysis options. For more
information about the requirements, see Requirements for Using
the GCOS Services, on page 587.
To change the Analysis Service options:
In the Settings shortcut bar, click the Defaults button
Select Tools → Defaults from the menu bar.
The Defaults dialog box appears.
2. Click the Analysis Settings tab (Figure E.9).
1.
Cell intensity analysis options
Figure E.9
Defaults dialog box, Analysis Settings tab
; or
appendix E | Configuring the GCOS Services
599
The Analysis settings are active only when GCOS is being used with
the GCOS Server option.
3.
Select the desired option from the radio buttons:
- Analyze intensity data on local workstation.
- Analyze intensity data on GCOS server.
If the analysis / transfer service on the client is running under the
windows local SYSTEM account, then the “Analyze data on local
workstation” radio button is disabled.
Click OK.
The selected changes are applied.
You can track the progress of the intensity data analyses and file
archiving in the CEL Analysis and Data Transfer window
(see page 133).
The other settings of the Analysis Settings tab are described in
Analysis Settings, on page 335.
4.
SETTING ARCHIVING OPTIONS FOR DAT FILES
DAT files may be stored locally or to a network location using the
GCOS Transfer Service. A JPG format file lets you view the image for
basic QC purposes.
The GCOS Transfer Service cannot be used when working with a
GCOS Server and when analysis is set to be done on the remote
server. Use GCOS Manager to archive the data.
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To change the Transfer Service options:
1.
In the Settings shortcut bar, click the Defaults button
Select Tools → Defaults from the menu bar.
The Defaults dialog box appears.
2.
Click the Archive Settings (Figure E.10).
; or
Figure E.10
Defaults dialog box, Archive Settings tab
Select the Archive data after scan checkbox to archive the DAT
files.
4. Enter a location in the Archive data location box; or
Click the Browse button and select a directory for the archived
files.
The software will not allow a UNC network location if the transfer
service is running under the local SYSTEM account.
3.
If the service is configured to run as a user who does not have
access to a networked location, the auto-archive will fail.
appendix E | Configuring the GCOS Services
5.
601
Click OK.
The selected changes are applied.
Experiments that make use of automation must bypass the analysis
service and data transfer service. All analysis in experiments that
make use of automation must occur on the GCOS server when
working in server mode.
Automation can only be used in conjunction with expression arrays.
You can track the progress of the intensity data analyses and file
archiving in the CEL Analysis and Data Transfer window
(see page 133).
You can view the JPG file in the Image Window (see The Image Viewer
with JPG Files, on page 217).
The archived data can be unarchived and made available using the
Unarchive command in GCOS Manager. For more information, see
Unarchiving Data, on page 361.
Setting the Start/Stop Service Policy
Both the user running the control applet and the specified 'Run As'
user must have Start/Stop services as part of the user's local system
policies. You will see a warning when trying to configure the system
if you do not have these policies set correctly (Figure E.11).
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Figure E.11
Error message
You will need to set the Start/Stopping Service policy so that your
domain user is in the group with these privileges, as explained in this
section.
If domain-level policy settings are defined, they override the local
policy settings. You will need to get the domain administrator to
change the domain-level policy settings in this case.
You do this in two sets of steps:
Check to see if you have administrator privileges on the computer
and get them added if necessary (see below).
2. Add the Administrators group to the Start/Stop Services policy
(see Adding the Administrators Group to the Start/Stop Service Policy, on
page 604).
After you have done these steps, you can set the GCOS Service options
and configure the GCOS software (see Configuring the GCOS Service
Settings, on page 589).
1.
CHECKING ADMINISTRATOR PRIVILEGES
To check to see if you are in the administrators group on the computer:
1.
Right-click on the My Computer icon and select Manage from
the pop-up menu.
The Computer Management window opens (Figure E.12).
appendix E | Configuring the GCOS Services
603
Figure E.12
Computer Management window
The window has a data tree on the left side with different objects.
Some parent objects may have child objects. The left side displays
a list of the child objects or other contents for the object selected
in the data tree.
2. Select System Tools → Local Users and Groups → Groups in
the tree.
A list of groups appears on the Name box on the right side of the
window (Figure E.12).
3. Click Administrators in the list.
The Administrators Properties dialog box opens (Figure E.13).
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Figure E.13
Administrators Properties dialog box
4.
Make sure your domain and user name are in the Members list. If
not, see your local CIS personnel to get your account added.
ADDING THE ADMINISTRATORS GROUP TO THE START/STOP SERVICE
POLICY
After making sure that you are in the Administrators group, you can
add the Administrators group to the Start/Stop Service policy.
1.
Click the Microsoft® Windows® Start button
select Settings → Control Panels.
The Control Panels window opens (Figure E.14).
, then
appendix E | Configuring the GCOS Services
Figure E.14
Control Panel window, Administrative Tools icon selected
2.
Double-click the Administrative Tools icon.
The Administrative Tools window opens (Figure E.15).
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Figure E.15
Administrative Tools window
3.
Double-click on the Local Security Policy icon.
The Local Security Policy window opens (Figure E.16).
Figure E.16
Local Security Settings window
appendix E | Configuring the GCOS Services
607
The data tree on the left side of the window displays a list of
objects. An object may itself have child objects. The right side of
the window displays child objects or other content for the object
selected in the data tree.
4. In the Security Settings tree, select Local Policies → User Rights
Assignment.
A list of user’s rights policies are displayed in the right-hand side
of the window (Figure E.16) with the following information:
Policy
Unique ID for the policy.
Local Setting
Users or groups assigned to the local policy settings.
Effective Setting
Users or groups assigned to the domain-level policy settings
(overrides the local policy settings).
If domain-level policy settings are defined and displayed in the
Effective Settings, they override the local policy settings. You will
need to get the domain administrator to change the domain-level
policy settings in this case.
5.
Double-click on the Log On as a Service policy
The Local Security Policy Setting dialog box for Log On as a
Service opens (Figure E.17).
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Figure E.17
Local Security Policy Setting dialog box
This dialog box lists the users and groups assigned to that policy.
If domain-level policy settings are defined, they override the local
policy settings. You will need to get the domain administrator to
change the domain-level policy settings in this case.
6.
Click the Add button.
The Select Users or Groups dialog box opens (Figure E.18).
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Figure E.18
Select Users or Groups dialog box
The Look In drop-down box displays a list of domains.
The Name box displays a list of the available users and groups in
the selected domain.
The bottom box displays users and groups selected for adding to a
policy.
7. Select the Administrators group.
8. Click the Add button in the Select Users or Groups dialog box.
The Administrators group is displayed in the lower box
(Figure E.19).
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Figure E.19
Select Users or Groups, administrator’s group selected
9.
Click the OK button in the Select Users or Groups dialog box.
The Select Users or Groups dialog box closes, and the
Administrators group is displayed in the Local Security Policy
Settings dialog box (Figure E.20).
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Figure E.20
Local Security Policy Setting, Administrators group added
10. Click
the OK button on the Local Security Policy Setting dialog
box.
11. The dialog box closes, and the Administrators group is displayed
in the Local Security Settings window, Log on as a Service policy
(Figure E.21).
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Figure E.21
Local Security Settings dialog box, Administrators group added to Log On as a
Service policy
12. Close
the Local Security Settings dialog box.
Setting the Act As Part of the Operating System Policy
If you are installing GCOS 1.4 on a computer with the Windows 2000
operating system, you will also need to set Act as Part of the Operating
System policy so that your domain user is in the group with these
privileges.
Both the user running the control applet and the specified 'Run As'
user must have Act as Part of the Operating System services as part of
the user's local system policies. You will see a warning when trying to
configure the system if you do not have these policies set correctly
(Figure E.22).
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Figure E.22
Error message
You will need to set the Act as Part of the Operating system policy so
that your domain user is in the group with these privileges, as
explained in this section.
If domain-level policy settings are defined, they override the local
policy settings. You will need to get the domain administrator to
change the domain-level policy settings in this case.
You do this in two sets of steps:
Check to see if you have administrator privileges on the computer
and get them added if necessary (see below).
2. Add the Administrators group to the Act as Part of the Operating
System policy (see Setting the Act As Part of the Operating System
Policy, on page 612
After you have done these steps, you can set the GCOS Service options
and configure the GCOS software (see Configuring the GCOS Service
Settings, on page 589).
1.
CHECKING ADMINISTRATOR PRIVILEGES
To check to see if you are in the administrators group on the computer:
1.
Right-click on the My Computer icon and select Manage from
the pop-up menu.
The Computer Management window opens (Figure E.23).
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Figure E.23
Computer Management window
The window has a data tree on the left side with different objects.
Some parent objects may have child objects. The left side displays
a list of the child objects or other contents for the object selected
in the data tree.
2. Select System Tools → Local Users and Groups → Groups in
the tree.
A list of groups appears on the Name box on the right side of the
window (Figure E.23).
3. Click Administrators in the list.
The Administrators Properties dialog box opens (Figure E.24).
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Figure E.24
Administrators Properties dialog box
4.
Make sure your domain and user name are in the Members list. If
not, see your local CIS personnel to get your account added.
ADDING THE ADMINISTRATORS GROUP TO THE ACT AS PART OF THE
OPERATING SYSTEM POLICY (WINDOWS 2000 ONLY)
After making sure that you are in the Administrators group, you can
add the Administrators group to the Act as Part of the Operating
System policy.
1.
Click the Microsoft® Windows® Start button
select Settings → Control Panels.
The Control Panels window opens (Figure E.25).
, then
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Figure E.25
Control Panel window, Administrative Tools icon selected
2.
Double-click the Administrative Tools icon.
The Administrative Tools window opens (Figure E.26).
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Figure E.26
Administrative Tools window
3.
Double-click on the Local Security Policy icon.
The Local Security Policy window opens (Figure E.27).
Figure E.27
Local Security Settings window
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The data tree on the left side of the window displays a list of
objects. An object may itself have child objects. The right side of
the window displays child objects or other content for the object
selected in the data tree.
4. In the Security Settings tree, select Local Policies → User Rights
Assignment.
A list of user’s rights policies are displayed in the right-hand side
of the window with the following information (Figure E.27):
Policy
Unique ID for the policy.
Local Setting
Users or groups assigned to the local policy settings.
Effective Setting
Users or groups assigned to the domain-level policy settings
(overrides the local policy settings).
If domain-level policy settings are defined and displayed in the
Effective Settings, they override the local policy settings. You will
need to get the domain administrator to change the domain-level
policy settings in this case.
5.
In the Local Security Settings dialog box, double-click on the Act
as part of the operating system policy (Figure E.28).
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Figure E.28
Local Security Settings, Act as part of the operating system policy selected
The Local Security Policy Setting dialog box for Act as part of the
operating system opens (Figure E.29).
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Figure E.29
Local Security Policy Setting dialog box, Act as part of the operating system
policy selected
This dialog box lists the users and groups assigned to that policy.
If domain-level policy settings are defined, they override the local
policy settings. You will need to get the domain administrator to
change the domain-level policy settings in this case.
6.
Click the Add button.
The Select Users or Groups dialog box opens (Figure E.30).
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Figure E.30
Select Users or Groups dialog box
The Look In drop-down box displays a list of domains.
The Name box displays a list of the available users and groups in
the selected domain.
The bottom box displays users and groups selected for adding to a
policy.
7. Select the Administrators group.
8. Click the Add button in the Select Users or Groups dialog box.
The Administrators group is displayed in the lower box
(Figure E.31).
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Figure E.31
Select Users or Groups, administrator’s group selected
9.
Click the OK button in the Select Users or Groups dialog box.
The Select Users or Groups dialog box closes, and the
Administrators group is displayed in the Local Security Policy
Settings dialog box (Figure E.32).
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Figure E.32
Local Security Policy Setting, Act as part of the operating system policy,
Administrators group added
10. Click
the OK button on the Local Security Policy Setting dialog
box.
11. The dialog box closes, and the Administrators group is displayed
in the Local Security Settings window, Act as part of the operating
system policy (Figure E.33).
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Figure E.33
Local Security Settings dialog box, Administrators group added to Act as part of
the operating system policy
12. Close
the Local Security Settings dialog box.
Appendix
F
Expression Algorithm, Expression
Analysis Metrics & Settings
Appendix
F
627
Expression Algorithm, Expression
Analysis Metrics & Settings
GCOS and versions of Microarray Suite higher than 5.0 run the Statistical
expression algorithm. Previous versions of Microarray Suite (lower
than 5.0) run the Empirical expression algorithm.
This appendix contains the following sections:
• Expression Analysis Algorithm (see below)
• Expression Analysis Metrics (see page 636)
• Expression Analysis Settings (see page 644)
• Cell Summary Report Algorithm (see page 679)
Expression Analysis Algorithm
Sections in the Algorithm Description:
• Notation (see below)
• Algorithm Output Definitions (see page 628)
• Background Subtraction (see page 629)
• Single-Array Expression Analysis (see page 630)
• Comparison Expression Analysis (see page 633)
• References (see page 635)
NOTATION
A GeneChip® probe array consists of a number of cells (square-shaped
areas on the array) and each contains many copies of a unique probe.
Probes are tiled in probe pairs consisting of a perfect match (PM) and
a mismatch (MM).
The sequence of the PM and MM are the same, except for a base
substitution in the middle of the MM probe sequence. A probe set
includes a series of probe pairs and represents an expressed transcript
(Figure F.1).
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Figure F.1
Probe set that includes 10 probe pairs
ALGORITHM OUTPUT DEFINITIONS
Signal
A measure of the abundance of a transcript.
Stat Pairs
The number of probe pairs for a particular probe set on the
array.
Stat Pairs Used
= Pairs - Masked probe pairs - Saturated MM probe pairs
This is the number of pairs used by the Statistical Expression
algorithm to make the detection call in an single-array
analysis.
Detection
The call in an single-array analysis that indicates if the
transcript was Present (P), Absent (A), Marginal (M), or No
call (NC).
Detection p-value
p-value that indicates the significance level of the Detection
call.
Stat Common Pairs
The intersection of the probe pairs from the baseline and
experiment that are used by the Statistical Expression
algorithm to make the Change call in a comparison analysis.
Change
The call that indicates the change in transcript level between
a baseline and an experiment array.
Change p-value
p-value that indicates the significance level of the Change
call.
Signal Log Ratio
The change in expression level for a transcript between a
baseline and an experiment array. This change is expressed as
the log2 ratio.
Signal Log Ratio low
The lower limit of the Log Ratio within a 95% confidence
range.
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629
Signal Log Ratio high The upper limit of the Signal Log Ratio within a 95%
confidence range.
BACKGROUND SUBTRACTION
The first step in the analysis is to correct for background across the
entire array. The calculated background establishes an intensity floor
that is subtracted from all intensity values.
Raw cell intensities → Background-adjusted intensities
The algorithm:
• divides the array into equally spaced zones (Figure F.2)
• assigns an average background to the center of each zone
• computes the distance from each cell to the center of every zone
• computes a weighting factor (the reciprocal of the sum of a
constant and the square of the distance from the cell to the zone
center)
• computes the background of each cell by applying the weighting
factor to the zone average (the average background assigned to the
center of each zone)
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Figure F.2
Array zones for computing background; the arrow color indicates the relative
weights
SINGLE-ARRAY EXPRESSION ANALYSIS
Detection
The Detection call answers the question: Is the transcript of a
particular probe set reliably detected by the probe array? We want an
answer of Absent or Present. In this context, Absent means the
expression level is below the threshold of detection. In the case of
uncertainty, we can get a Marginal call.
Detection call results are easy to filter and interpret. For example, we
may only want to look at genes whose transcripts are Present in a
particular experiment. An additional advantage is that the Detection
and the Signal values are calculated using independent algorithms that
add additional information to the results.
Raw cell intensities → Absent, Present, or Marginal Detection
call plus p-values
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A No Call detection result occurs if all of the probe pairs of a probe
set are excluded from the analysis. A probe pair is excluded if the
PM or MM is masked or if the MM is saturated.
Discrimination Value
The algorithm computes a discrimination value that is used as a filter
to remove from further consideration all probe sets with insignificant
differences between PM and MM.
discrimination value = (PM - MM)/(PM + MM)
The median of the discrimination ratios of all the probe pairs of a
probe set is compared to a user-modifiable parameter τ (default =
0.015), and produces an intermediate call.
Increasing τ can reduce the number of false Present calls, but may
also reduce the number of true Present calls.
Making the Call
A one-sided Wilcoxon’s Signed Rank test is used to calculate a p-value
that reflects the significance of the differences between PM and MM.
The p-value or statistical significance of a result is the probability that
the observed change in a sample occurred by pure chance. For example,
a p-value of 0.05 means there are five chances in 100 that the results
are not significant. The lower the p-value, the greater the probability
that the results are significant.
To make a call, the p-value for a probe set is examined on an axis with
two user-definable thresholds, α1 and α2 (defaults α1 = 0.04 and α2 =
0.06). For p-values between zero and 0.5, α1and α2 define the
thresholds for the calls (Figure F.3). See also Table F.1.
The result is reported as the Detection call that is associated with the
calculated p-value.
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Decreasing the significance level α1 can reduce the number of false
detected calls and reduce the number of true detected calls.
Increasing the significance level α2 can reduce the number of false
undetected calls and reduce the number of true undetected calls.
Figure F.3
User-modifiable thresholds, α1 and α2
Table F.1
Statistical algorithm Detection call rules
Computed Detection p-values
Detection Call
p < α1
Present
α1 ≤ p < α2
p ≥ α2
Marginal (at the limit
of detection)
Absent
Calculating the Signal
The signal represents the amount of transcript in solution.
Background-adjusted cell intensities → Probe set signal
For each PM intensity, a matching MM probe provides a reference
background hybridization intensity. If the MM value is less than the
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633
PM value, the algorithm uses the MM value directly. However, if the
MM value is larger than the PM value, the algorithm creates an
adjusted MM value based on the average difference intensity between
log2 PM and log2 MM, or if that measure is too small, some fraction of
PM.
The adjusted MM values are used to calculate the log2 PM - log
adjusted MM for each probe pair. The Signal for a probe set is
calculated as the one-step biweight estimate of the combined
differences of all the probe pairs in the probe set.
COMPARISON EXPRESSION ANALYSIS
A comparison analysis compares the expression levels of the transcripts
on one array to those on another. By directly comparing matching cells
on two arrays, any inherent differences in hybridization efficiency will
cancel out. As a result, this is an accurate and sensitive method of
determining changes in expression levels.
Differences between PM and MM and Differences between PM
and Background (Experiment and Baseline) → Change call and
p-value
The algorithm computes a primary normalization factor and two
additional normalization factors that straddle the primary
normalization factor. The spread between the normalization factors is
determined by the perturbation parameter (d).
To determine the p-values, a signed rank analysis is carried out on the
PM and MM differences for each probe pair in a probe set from the two
arrays in the comparison. The resulting p-values are used to make the
change calls.
To make a call, the p-value for a probe set is examined on an axis with
four thresholds (Figure F.4). For p-values between zero and 1.0, γ1and
γ2 define the thresholds for the calls.
The result is reported as the Change call that is associated with the
calculated p-value (see Table F.2). The output p-value is the critical pvalue. The critical p-value is the p-value that determines the Change
call.
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The critical p-value, p, is defined by the following:
• p = max(p0, p1, p2), if p0 < 0.5, p1 < 0.5 and p2 < 0.5
• p = min(p0, p1, p2), if p0 > 0.5, p1 > 0.5 and p2 > 0.5
• p = 0.5, otherwise
Figure F.4
User-modifiable parameters, γ1 and γ2
Table F.2
Statistical algorithm Change call rules
Computed
Change p-values
p0 < γ 1
p1 < γ 1
p2 < γ 1
p0 < γ 2
p1 < γ 2
p2 < γ 2
Else
p0 > 1-γ2
p1 > 1-γ2
p2 > 1-γ2
p0 > 1-γ1
p1 > 1-γ1
p2 > 1-γ1
Change call
Increasing
Marginally increasing
No change
Marginally decreasing
Decreasing
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635
You may adjust γ1 and γ2 by specifying different values for: γ1L, γ1H, γ2L,
γ2H. See Expression Analysis Settings, on page 644.
Decreasing γ1 can reduce the number of false Increase and Decrease
calls, but can also reduce the number of true Increase and Decrease
calls. Increasing γ2 can reduce the number of false No-Change calls, but
can also reduce the number of true No-Change calls. Increasing the
perturbation parameter (d) can increase the number of true NoChange calls, but can also increase the number of false No-Change
calls.
A No Call occurs if all of the probe pairs of a probe set are excluded
from the analysis. A probe pair is excluded if the PM or MM in the
experiment or baseline is masked or saturated.
Signal Log Ratio
Probes inherently hybridize with slightly different affinities. Relative
expression values compare identical probes in the baseline and
experiment. As a result, probe specific effects are canceled out.
Adjusted cell intensities (Baseline and Experiment) → Signal Log
Ratio, Signal Log Ratio low, and Signal Log Ratio high
The Signal Log Ratio calculation is an extension of the signal
calculation. The discrimination of the log2 ratio is used to correct for
outlier probes. The one-step biweight method is used to compute the
average log2 ratio of the probe set. The upper and lower limits of the
95th confidence interval are reported as Signal Log Ratio high and
Signal Log Ratio low.
REFERENCES
Hoaglin, D.C., Mosteller, R., Tukey, J.W. 2000. Understanding
Robust and Exploratory Data Analysis, John Wiley & Sons, New
York.
2. Hollander, M., Wolfe, D.A. 1999. Nonparametric Statistical Methods
(second edition), John Wiley & Sons, New York.
1.
636
3.
Affymetrix® GeneChip® Operating Software User’s Guide
Liu, W.M., Mei, R., Bartell, D.M., Di, X., Webster, T.Q., Ryder,
T. 2001. Rank-based algorithms for analysis of microarrays,
Proceedings SPIE, 4266.
Wilcoxon, F. 1945. Individual comparisons by ranking methods.
Biometrics.1:80-83.
5. Roderick, J.A., Little, D., Rubin, B. 1987. Statistical Analysis With
Missing Data. John Wiley & Sons, New York.
4.
Expression Analysis Metrics
GCOS and versions of Microarray Suite higher than 5.0 run the
Statistical expression algorithm. Versions of Microarray Suite (lower
than 5.0) run the Empirical expression algorithm. The metrics for
these algorithms are described in the following sections:
• Statistical Expression Algorithm, on page 636
• Empirical Expression Algorithm, on page 638
STATISTICAL EXPRESSION ALGORITHM
Single-Array Results
Signal
A measure of the abundance of a transcript.
Detection
The call that indicates whether the transcript is detected (P, Present),
undetected (A, Absent), or at the limit of detection (M, Marginal).
Detection p-value
p-value that indicates the significance of the Detection call.
Stat Pairs
The number of probe pairs for a particular probe set on an array.
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637
Stat Pairs Used
The number of probe pairs per probe set used in the analysis. This may
be the total number of probes per probe set on the probe array or the
number of probe pairs in a pre-designated subset (for example, probe
pairs specified by a probe mask file and/or a masked image). Stat Pairs
Used = total probe pairs per probe set – (probe pairs masked in a mask
file) – (probe pairs masked in the image) – (saturated MM probe pairs).
Comparison Results
Signal Log Ratio
The change in the expression level of a transcript between a baseline
and an experiment array. This change is expressed as the log2 ratio. A
log2 ratio of 1 is equal to a fold change of 2.
Signal Log Ratio Low
The lower limit of the Log Ratio within a 95% confidence interval.
Signal Log Ratio High
The upper limit of the Log Ratio within a 95% confidence interval.
Change
The call that indicates the change in the transcript level between a
baseline and experiment (Increase (I), Marginal Increase (MI), No
Change (NC), Marginal Decrease (MD), Decrease (D))
Change p-value
p-value that indicates the significance of the Change call.
Stat Common Pairs
The intersection of the probe pairs from the baseline and experiment
that are used by the Expression algorithm to make the Change call in
a comparison analysis.
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EMPIRICAL EXPRESSION ALGORITHM
Versions of Microarray Suite lower than 5.0 run the Empirical
Expression algorithm.
Single-Array Analysis Results
Positive & Negative
The number of probe pairs scored positive or negative. A probe pair is
called positive if the intensity of the PM probe cell is significantly
greater than that of the corresponding MM probe cell. A probe pair is
called negative if the intensity of the MM probe cell is significantly
greater than that of the corresponding PM probe cell. To evaluate the
intensity, the algorithm calculates the ratio and difference associated
with each probe pair and compares these values to the Statistical
Difference Threshold (SDT) and the Statistical Ratio Threshold (SRT).
A probe pair is Positive if: PM – MM > SDT and PM/MM > SRT
A probe pair is Negative if: MM – PM > SDT and MM/PM > SRT
The SDT is a function of the noise (Q) and is calculated by the
software: SDT = Q * SDTmult. The SDTmult and the SRT are usermodifiable parameters. The SDTmult is set at 2.0 for the standard
staining protocol or 4.0 for the antibody amplification protocol. (Refer
to the Expression Analysis Technical Manual or the HuSNP® Mapping
Assay User Manual). The default SRT value is 1.5.
Increasing the SDTmult and SRT increases analysis stringency,
reducing these thresholds decreases analysis stringency.
The number of positive and negative probe pairs is determined for
every probe set and are used to derive parameters that describe probe
set performance.
Pairs
The number of probe pairs for a particular probe set on an array.
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639
Pair Used
The number of probe pairs per probe set used in the analysis. This may
be the total number of probes per probe set on the probe array or the
number of probe pairs in a pre-designated subset (for example, probe
pairs specified by a probe mask file and/or a masked image).
Pairs Used = total probe pairs per probe set – (probe pairs masked in
a mask file) – (probe pairs masked in the image).
Pairs in Avg
A trimmed probe set that excludes probes with extremely intense or
weak signal from the analysis. If 8 or fewer probe pairs are used, Pairs
in Avg = Pairs Used (or the number of probe pairs per probe set minus
any that are masked).
Super scoring is performed if more than 8 probe pairs are used.
Superscoring is a process that excludes probe pairs from calculation of
the Avg Diff and Log Avg Ratio if they are outside a given intensity
range. Microarray Suite calculates the mean and standard deviation of
the intensity differences (PM – MM) for an entire probe set (excluding
the highest and lowest values). Those values within a set number of
standard deviations (STP) are included in the calculation of the Avg
Diff or Log Avg Ratio. The STP is a user-modifiable parameter with a
default value = 3.
Pos Fraction
# positive probe pairs/# probe pairs used
Log Avg
Describes the hybridization performance of a probe set and is
determined by calculating the ratio of the PM/MM intensities for each
probe pair in a probe set, taking the logs of the resulting values, and
averaging them for the probe set:
Log Avg = 10 x {[Σ log (PM/MM)] / Pairs in Avg}
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Log Avg = 0 indicates random cross hybridization. The higher the
Log Avg, the more confidence the transcript is present.
Pos/Neg
The ratio of Positive probe pairs to Negative probe pairs in a probe set
(# Positive probe pairs / # Negative probe pairs).
Avg Diff
∑ ( PM – M M )
A vg D iff = -----------------------------------Pairs in A vg
This parameter serves as a relative indicator of the level of expression
of a transcript. It is used to determine the change in the hybridization
intensity of a given probe set between two different experiments.
The Avg Diff is calculated by taking the difference between the PM
and MM of every probe pair (excluding the probe pairs where PM –
MM is outside the STP standard deviation of the mean of PM-MM) in
a probe set and averaging the differences for the entire probe set.
The Avg Diff cannot be used to compare the hybridization intensity
levels of two different probe sets on the same array.
Absolute Call
Each transcript in an single-array analysis has three possible Absolute
Call outcomes: Present (P), Absent (A), or Marginal (M). The Absolute
call is derived from the Pos/Neg, Positive Fraction, and Log Avg
Absolute call metrics. Each Absolute call metric is weighted and
entered into a decision matrix to determine the status of the transcript.
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641
Comparison Analysis Results
Increase
A probe pair is considered to increase if the intensity difference
between the PM and MM probe cells in the experimental sample is
significantly higher than in the baseline sample. Two criteria must be
met for a probe pair to show a significant increase:
(PM – MM)exp – (PM – MM)base > Change Threshold (CT), and
[(PM – MM)exp – (PM – MM) base] / max [Q/2, min(|PM – MM|exp |PM
– MM|base)] > Percent Change Threshold/100
Decrease
A probe pair is considered to decrease if the intensity difference
between the PM and MM probe cells in the experimental sample is
significantly lower than in the baseline sample. Two criteria must be
met for a probe pair to show a significant decrease:
(PM – MM) base – (PM – MM) exp > Change Threshold (CT), and
[(PM – MM)base – (PM – MM) exp] / max [Q/2, min(|PM – MM|exp, |PM
– MM|base)] > Percent Change Threshold/100
The software calculates the Change Threshold (CT) using the SDT
(Statistical Difference Threshold) of both the experimental and
baseline data. Alternatively, the user may define the CT by entering a
value for the CT Multiplier (in the Parameters tab of the Expression
Analysis Settings dialog box), which is multiplied by the noise (Q) of
the baseline or experimental data, whichever is greater. The Percent
Change Threshold is a user-specified value (also set in the Parameters
tab of the Expression Analysis Settings dialog box).
Inc Ratio
For each transcript: # Increased probed pairs / # probe Pairs Used
Dec Ratio
For each transcript: # Decreased Probe pairs / # probe Pairs Used
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Pos Change
Positive probe pairsexp - # Positive probe pairsbaseline
Neg Change
Negative probe pairsexp - # Negative probe pairsbaseline
Inc/Dec
For each transcript: the # increased probe pairs / # decreased probe
pairs
DPos-DNeg Ratio
(Positive Change – Negative Change)/# probe Pairs Used
The DPos – DNeg Ratio and Log Avg Ratio Change are usually
positive when a transcript changes from a very low to a relatively high
expression level and are typically negative when the expression level
changes from a high to a very low or undetectable level. Both metrics
may have values close to zero if the transcript is present in both the
baseline and experimental samples despite an increase or decrease in
the level of the transcript.
Log Avg Ratio Change
Log Avgexp – Log Avgbase
The difference between the Log Avg Ratio of the baseline and
experimental probe array data (in a comparison analysis) for each
transcript. The Log Avg Ratios are recomputed for each for each probe
set based on probe pairs used in both the baseline and experimental
probe arrays (the recomputed values are not displayed by the software).
Difference Call
Each transcript in a comparison analysis has five possible Difference
Call outcomes: (1) Increase (I), (2) Marginally Increase (MI), or (3)
Decrease (D), (4) Marginally Decrease (MD), and (5) No Change (NC).
The difference call is derived from the comparison metrics: Max
[Increase/Total, Decrease/Total], Increase/Decrease Ratio, Log
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643
Average Ratio Change, and Dpos – Dneg Ratio. Each comparison
metric is weighted and entered into a decision matrix to determine the
status of the transcript.
Avg Diff Change
The Avg Diff values are recomputed for each probe set based on probe
pairs used in both the baseline and experimental probe arrays (the
recomputed values are not displayed by the software).
Avg Diff Change = Avg Diffexp – Avg Diffbaseline
B=A
An asterisk (*) in this column indicates the transcript is called absent
(A) in the baseline.
Fold Change
The Fold Change indicates the relative change in the expression levels
between the experiment and baseline targets. The Fold Change for a
transcript is a positive number when the expression level in the
experiment increases compared to the baseline and is a negative
number when the expression level in the experiment declines. The
Fold Change (FC) is calculated as:
⎧ +1 if ( AvgDiff
≥ AvgDiff
)⎫
⎛
⎞ ⎪
exp
base ⎪
( AvgDiffChange )
FC = ⎜ ----------------------------------------------------------------------------------------------------------------------------⎟ + ⎨
⎬
< AvgDiff
)
⎝ max [ min (AvgDiff base,AvgDiff exp), Q M × Q C ]⎠ ⎪ -1 if ( AvgDiff
exp
base ⎪⎭
⎩
The normalized or scaled Avg Diff values are recomputed in both the
experimental and baseline data sets to include only probe pairs used in
both the baseline and experiment arrays. Then the Avg Diff Change is
calculated as:
Avg Diff Change = Avg Diffexp - Avg Diffbase
QC = max(Qexp, Qbase)
QM = 2.1 for a 50µm feature or 2.8 for a 24µm feature
If the noise (Q) of the experiment or baseline array is greater than the
Avg Diff of the transcript (the baseline or experimental data), the Fold
Change is calculated over the noise and is an approximation [a tilde
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character (~) precedes the approximated Fold Change value in the
*.chp file].
Sort Score
The Sort Score is a ranking based on the Fold Change and the Avg Diff
Change. The higher the Fold Change and the Avg Diff Change, the
higher the Sort Score.
Expression Analysis Settings
The expression analysis settings are user-modifiable variables with
defaults empirically determined by Affymetrix. They are organized by
the tabs of the Expression Analysis Settings dialog box:
• Scaling Tab, on page 645
• Normalization Tab, on page 655
• Probe Mask Tab, on page 665
• Baseline Tab, on page 674
• Parameters Tab, on page 677
The Expression algorithm relies on these settings to derive
biologically meaningful results from the hybridization intensity data.
To view the expression analysis settings:
1.
Click Analysis Settings in the shortcut bar, then click
Expression ; or
Select Tools → Analysis Settings → Expression from the menu
bar.
The Expression Analysis Settings dialog box appears (Figure F.5).
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Figure F.5
Expression Analysis Settings, Scaling tab, User Defined scaling option selected
Make a selection from the Probe Array Type drop-down list.
The settings are specific for the selected probe array type and do
not affect the settings for other types of probe arrays.
3. Click a tab to view the different types of expression analysis
settings for the selected probe array type.
2.
SCALING TAB
Scaling is a mathematical technique applied to the data from several
different probe arrays (of the same type) to minimize discrepancies due
to variables such as sample preparation, hybridization conditions,
staining, or probe array lot. The Scale Factor is also applied to the noise
value.
GCOS offers three types of scaling: User Defined, All Probe Sets, and
Selected Probe Sets.
To view the scaling settings:
• Click the Scaling tab in the Expression Analysis Settings dialog
box (Figure F.5).
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• Make a selection from the Probe Array Type drop-down list.
User Defined Scaling
The User Defined scaling option multiplies the signal of each probe
set on the array by a user-specified scale factor.
1.
In the Scaling tab, choose the User Defined option (Figure F.6).
Figure F.6
Expression Analysis Settings, Scaling tab, User Defined scaling option with no
scaling specified (scale factor = 1)
2.
Enter a number in the Scale Factor box.
A scale factor of one is equivalent to no scaling.
3.
Click OK to close the Expression Analysis Settings dialog box.
All Probe Sets Scaling
The All Probe Sets scaling option adjusts the trimmed mean signal
of a probe array to a user-specified target signal value.
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647
The single-array analysis results (*.chp) from different experiments
(probe arrays of the same type) that are scaled to the same target signal
using the All Probe Sets scaling option may be directly compared.
1.
In the Scaling tab, choose the All Probe Sets scaling option
(Figure F.7).
Figure F.7
Expression Analysis Settings, Scaling tab, All Probe Sets scaling option selected
Enter a target signal value.
3. Click OK to close the Expression Analysis Settings dialog box.
GCOS examines all of the probe sets on the array to compute the
trimmed mean signal and derive a scale factor for the array so that:
Target Signal = Scale Factor x Trimmed Mean Signalprobe array
The scale factor standardizes the trimmed mean signal of the array
to the target signal (Figure F.8).
2.
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Figure F.8
Scale factors (SF) standardize the average signal of each experiment to a userspecified target signal
Selected Probe Sets Scaling
The Selected Probe Sets scaling option adjusts the trimmed mean
signal of selected probe sets on a probe array to a user-specified target
signal value.
You can directly compare the single-array analysis results (*.chp) of
different experiments (probe arrays of the same type) if the same probe
sets have been scaled to the same target signal in each experiment
using the Selected Probe Sets scaling option.
For this scaling option, GCOS utilizes user-selected probe sets
(specified by a Scale Factor mask file) to calculate the trimmed mean
signal and derive the scale factor for the probe array so that:
Target Signal = Scale Factor x Trimmed Mean Signalselected probe sets
The scale factor standardizes the trimmed mean signal of an array to
the target signal (Figure F.8). Selected Probe Sets scaling does not
change the single-array call because the software also multiplies the
intensity of each probe set and the probe array noise by the scale factor.
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Creating a Scale Factor Mask File
1.
In the Scaling tab, choose the Selected Probe Sets option
(Figure F.9).
Figure F.9
Expression Analysis Settings, Scaling tab, Selected Probe Sets scaling option
2.
Enter a Target Signal value, then click Create/Open Probe Set
Mask.
The Probe Set Mask File dialog box displays existing mask files
(Figure F.10).
Mask files (*.msk) include Scale Factor, Normalization, and Probe
mask files. Each type of mask file has a different function and is
created in a separate tab of the Expression Analysis Settings dialog
box.
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Figure F.10
Probe Set Mask Definition dialog box
3.
Enter a name for the scale factor mask file in the File name box,
then click Open.
The Probe Set Mask Definition dialog box appears (Figure F.11).
Figure F.11
Probe Set Mask Definition dialog box
4.
To select probe sets for the mask file:
A.
Highlight the desired probe set names in the Exclude list.
B.
Click Include.
This adds the selected probe set names to the Include list for
the scale factor mask file.
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5.
651
To remove a probe set name(s) from the Include list:
Highlight the name(s) in the Include list.
B. Click Exclude.
Include All automatically moves all of the probe set names from
the Exclude list to the Include list.
Exclude All automatically Moves all of the probe set names from
the Include list to the Exclude list.
A.
6.
Click OK when finished to create the scale factor mask file and
close the Probe Set Mask Definition dialog box.
Selecting a Scale Factor Mask File
1.
In the Scaling tab, choose the Selected Probe Sets option
(Figure F.12).
Figure F.12
Expression Analysis Settings, Scaling tab, Selected Probe Sets option
2.
Click Browse (Figure F.12).
The Probe Set Mask File dialog box appears (Figure F.13).
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Figure F.13
Probe Set Mask File dialog box
Mask files (*.msk) are specific for the probe array type. GCOS will
not open a mask file that is incompatible with the currently selected
probe array type.
3.
Double-click the desired *.msk file.
The Expression Analysis Settings dialog box displays the currently
selected *.msk file name in the Scale Factor Mask File box
(Figure F.14).
appendix F | Expression Algorithm, Expression Analysis Metrics & Settings
Figure F.14
Expression Analysis Settings, Scaling tab, scale factor mask file selected
Editing a Scale Factor Mask File
1.
In the Scaling tab, choose the Selected Probe Sets option
(Figure F.15).
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Figure F.15
Expression Analysis Settings, Scaling tab, Selected Probe Sets option
2.
Click Create/Open Probe Set Mask.
The Probe Set Mask File dialog box appears (Figure F.16).
Figure F.16
Probe Set Mask File dialog box
3.
Double-click the desired *.msk file.
The Probe Set Mask Definition dialog box appears (Figure F.17).
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655
The Include list displays the probe sets included in the scale factor
mask file. The Exclude list displays probe sets not included in the
scale factor mask file.
Figure F.17
Probe Set Mask Definition dialog box
4.
To remove a probe set(s) from the *.msk file:
Highlight the probe set name(s) in the Include list.
B. Click Exclude.
5. To add a probe set(s) to the *.msk file, highlight the probe set
name(s) in the Exclude list, then click Include.
Include All automatically moves all of the probe set names from
the Exclude list to the Include list.
Exclude All automatically moves all of the probe set names from
the Include list to the Exclude list.
6. Click OK when finished to close the Probe Set Mask Definition
dialog box.
A.
NORMALIZATION TAB
Normalization is a mathematical technique similar to scaling that
enables comparison analysis of an experiment and baseline array.
GCOS offers three types of normalization: User Defined, All Probe
Sets, or Selected Probe Sets normalization. All Probe Sets or Selected
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Probe Sets normalization minimizes discrepancies between an
experiment and baseline array due to variables such as sample
preparation, hybridization conditions, staining, or probe array lot.
User Defined Normalization
User Defined normalization multiplies the signal of each probe set on
an array by a user-specified normalization value.
1.
In the Normalization tab, choose the User Defined option
(Figure F.18).
Figure F.18
Expression Analysis Settings, Normalization tab, User Defined normalization
option with no normalization specified (Normalization Value = 1)
2.
Enter a value in the Normalization Value box.
A normalization factor of one is equivalent to no normalization.
3.
Click OK to close the Expression Analysis Settings dialog box.
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All Probe Sets Normalization
All Probe Sets normalization adjusts or normalizes the trimmed mean
signal of the experiment to the trimmed mean signal of the baseline
(Figure F.19).
Figure F.19
Normalization Value normalizes the average signal of the experiment to the
average signal of the baseline
1.
In the Normalization tab, choose the All Probe Sets
normalization option (Figure F.20).
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Figure F.20
Expression Analysis Settings, Normalization tab, All Probe Sets normalization
option
2.
Click OK to close the Expression Analysis Settings dialog box.
The software examines all probe sets on the experiment or baseline
array to compute a trimmed mean signal for the experiment and a
trimmed mean signal for the baseline.
It computes a normalization value so that:
Trimmed Mean Signalbaseline = (Normalization Value) x (Trimmed
Mean Signalexperiment)
Selected Probe Sets Normalization
Selected Probe Sets normalization adjusts or normalizes the trimmed
mean signal of the experiment to the trimmed mean signal of the
baseline (Figure F.19).
For this normalization option, GCOS utilizes user-selected probe sets
(specified by a normalization mask file) to compute the trimmed mean
signal of the experiment and baseline, and derive a normalization value
so that:
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659
Trimmed Mean Signalbaseline selected probe sets = Normalization Value x
Trimmed Mean Signalexperiment selected probe sets
Creating a Normalization Mask File
1.
In the Normalization tab, choose the Selected Probe Sets option
(Figure F.21).
Figure F.21
Expression Analysis Settings, Normalization tab, Selected Probe Sets option
2.
Click Create/Open Probe Set Mask.
The Probe Set Mask File dialog box appears (Figure F.22).
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Figure F.22
Probe Set Mask File dialog box
The mask files (*.msk) include Scale Factor, Normalization, or
Probe mask files. Each type of mask file has a different function and
is created in a separate tab of the Expression Analysis Settings
dialog box.
3.
Enter a name for the new normalization mask file in the File name
box and click Open.
The Probe Set Mask Definition dialog box appears (Figure F.23).
Figure F.23
Probe Set Mask Definition dialog box
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661
Highlight the desired probe set names in the Exclude list. Click
Include to add them to the Include list for the new *.msk file.
5. To remove a probe set name(s) from the Include list, highlight the
name(s) in the Include list, then click Exclude.
Include All automatically moves all of the probe set names from
the Exclude list to the Include list.
Exclude All automatically moves all of the probe set names from
the Include list to the Exclude list.
4.
6.
Click OK when finished to create the normalization mask file and
close the Probe Set Mask Definition dialog box.
Selecting a Normalization Mask File
1.
In the Normalization tab, click Browse (Figure F.24).
The Probe Set Mask File dialog box appears (Figure F.25).
Figure F.24
Expression Analysis Settings, Normalization tab, Selected Probe Sets option
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Figure F.25
Probe Set Mask File dialog box
Mask files are specific for the probe array type. GCOS will not open
a mask file that is incompatible with the currently selected probe
array type.
2.
Double-click the desired *.msk file.
The Probe Set Mask File dialog box closes and the Expression
Analysis Settings dialog box displays the selected *.msk in the
Normalization Mask File box (Figure F.26).
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663
Figure F.26
Expression Analysis Settings, Normalization tab, normalization mask file
selected
Editing a Normalization Mask File
1.
In the Normalization tab, choose the Selected Probe Sets option
(Figure F.27).
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Figure F.27
Expression Analysis Settings, Normalization tab, Selected Probe Sets option
2.
Click Create/Open Probe Set Mask (Figure F.27).
The Probe Set Mask File dialog box appears (Figure F.28).
Figure F.28
Probe Set Mask File dialog box
3.
Double-click the desired *.msk file.
The Probe Set Mask Definition dialog box appears (Figure F.29).
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The Include list displays the probe sets included in the *.msk file.
The Exclude list displays the probe sets not included in the *.msk
file.
Figure F.29
Probe Set Mask Definition dialog box
4.
To remove a probe set(s) from the *.msk file:
Highlight the probe set name(s) in the Include list.
B. Click Exclude.
5. To add a probe set(s) to the *.msk file:
A.
Highlight the probe set name(s) in the Exclude list
B. Click Include.
Include All automatically moves all of the probe set names from
the Exclude list to the Include list.
Exclude All automatically moves all of the probe set names from
the Include list to the Exclude list.
6. Click OK when finished to close the Probe Set Mask Definition
dialog box.
A.
PROBE MASK TAB
User-selected probe pairs may be excluded or masked from an
expression analysis. In the Probe Mask tab (Figure F.30), you can
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create a probe mask file that specifies the probe pairs to exclude from
an analysis.
Figure F.30
Expression Analysis Settings, Probe Mask tab
Creating a Probe Mask
1.
In the Probe Mask tab, click Create/Open Probe Mask
(Figure F.30).
The Probe Mask File dialog box appears (Figure F.31).
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Figure F.31
Probe Mask File dialog box
The *.msk files include Scale Factor, Normalization, or Probe mask
files. Each type of mask file has a different function and is created
in a separate tab of the Expression Analysis Settings dialog box.
2.
Enter a name for the new probe mask file in the File name box and
click Open.
The Probe Mask Definition dialog box appears (Figure F.32) and
displays the probe array type and the probe mask name.
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Figure F.32
Probe Mask Definition dialog box
Select the desired probe set name from the Probe Sets drop-down
list and enter the desired probe pair numbers in the Probe Pairs
field (following the example format: 1-4,7,15,19).
These probe pairs will be omitted from the analysis.
4. Click the box below the Probe Sets drop-down list to add the
probe pairs to the probe mask (Figure F.33).
3.
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669
Figure F.33
Probe pairs selected for the probe mask file
Repeat Step 3 and Step 4 to specify additional probe pairs for the
probe mask.
6. Click OK when finished adding probe pairs to the probe mask.
5.
Selecting a Probe Mask
1.
In the Probe Mask tab, choose the Use Probe Mask File option
(Figure F.34).
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Figure F.34
Expression Analysis Settings, Probe Mask tab
2.
Click Browse.
The Probe Mask File dialog box appears (Figure F.35).
Figure F.35
Probe Mask File dialog box
3.
Double-click the desired probe mask.
The Probe Mask tab displays the selected probe mask
(Figure F.36).
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671
Mask files are specific for the probe array type. GCOS will not open
a mask file that is incompatible with the currently selected probe
array type.
Figure F.36
Expression Analysis Settings, Probe Mask tab
Editing a Probe Mask
1.
In the Probe Mask tab, click Create/Open Probe Mask
(Figure F.37).
The Probe Mask File dialog box appears (Figure F.38).
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Figure F.37
Expression Analysis Settings
Figure F.38
Probe Mask File dialog box
2.
Click the desired probe mask file and click OK (or double-click
the file name).
The Probe Mask Definition dialog box displays the probe pairs in
the selected probe mask (Figure F.39).
appendix F | Expression Algorithm, Expression Analysis Metrics & Settings
Figure F.39
Probe Mask Definition dialog box
3.
Click the probe set/probe pair entry you wish to edit.
The Probe Sets and Probe Pairs box automatically display the
selection (Figure F.40).
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Figure F.40
Edit entries in the Probe Pairs box and click the lower box (left) to update the probe pair list (right)
4.
Edit or delete the entry in the Probe Pairs field, then click the
lower field to update the list of probe pairs (Figure F.40).
5.
Click OK when finished to close the Probe Mask Definition dialog
box.
BASELINE TAB
In the baseline tab, the user selects the analysis output file (*.chp) that
will serve as the baseline in a comparison expression analysis
(Figure F.41).
Do not choose the Use Baseline Comparison Data option for an
single-array analysis.
1.
In the Baseline tab, choose the Use Baseline Comparison Data
option (Figure F.41).
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675
Figure F.41
Expression Analysis Settings, Baseline tab
2.
Click Browse.
The Baseline Comparison File dialog box appears (Figure F.42).
The baseline file must be derived from the same type of probe array
selected in the Probe Array Type drop-down list in the Expression
Analysis Settings dialog box (Figure F.41).
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Figure F.42
Baseline Comparison File dialog box
3.
Double-click the baseline *.chp and click Open.
The Baseline tab displays the selected baseline file for comparison
analyses (Figure F.43).
Figure F.43
Expression Analysis Settings, Baseline tab
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677
PARAMETERS TAB
The Parameters tab displays user-modifiable Statistical Expression
algorithm parameters (Figure F.44). Table F.3 describes the
parameters.
Versions of Microarray Suite lower than 5.0 run the Empirical
Expression algorithm. (for more information about the Empirical
Expression algorithm, see Expression Analysis Metrics, on
page 636.)
Figure F.44
Expression Analysis Settings, Parameters tab
The parameter default values were determined through extensive
empirical testing at Affymetrix. Changing a parameter value affects
the:
• algorithm output (for more information about the Statistical and
Empirical Expression algorithm outputs, see Appendix F,
Expression Analysis Metrics, on page 636)
• assay sensitivity (ability to make true Detection or Change calls)
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• assay specificity (ability to minimize false Detection or Change
calls)
Table F.3
User-modifiable Statistical Expression algorithm parameters
Parameter
Alpha1 (α1)
Alpha2 (α2)
Tau (τ)
Description
Effect of Changing Parameter
The p-value threshold that defines Present
and Marginal Detection calls.
If: p < α1 the call is Present
α1 < p < α2 the call is Marginal
Decreasing α1 may reduce the number of
false Present calls (increases specificity)
and the number of true Present calls
(decreases sensitivity).
The p-value threshold that defines Marginal
and Absent Detection calls.
If: α1 < p < α2 the call is Marginal
p > α2 the call is Absent
Increasing α2 may reduce the number of
false Absent calls (increases sensitivity)
and the number of true Absent calls
(decreases specificity).
Threshold for the probe set discrimination
score. If the discrimination score < τ, the
difference between the PM and MM cells in
the probe set is considered insignificant.
The algorithm does not make a call for the
probe set.
Gamma1L (γ1L)
The lower limit of γ1 which is the p-value
threshold that defines Increase and
Marginal Increase Change calls.
Gamma1H (γ1H)
The upper limit of γ1 which is the p-value
threshold that defines Increase and
Marginal Increase Change calls.
Gamma2L (γ2L)
The lower limit of γ2 which is the p-value
threshold that defines Marginal Increase
and No Change calls.
Gamma2H (γ2H)
The upper limit of γ2 which is the p-value
threshold that defines marginal, No Change
and Change calls.
Perturbation (d)
Determines the spread between the three
normalization factors the algorithm
computes for an experiment and baseline in
a comparison analysis.
Increasing τ may reduce the number of
false Present calls (increases specificity)
and the number of true Present calls
(decreases sensitivity).
Decreasing γ1L and γ1H decreases γ1.
Decreasing γ1 may reduce the number of
false Increase and Decrease calls
(increases specificity) and may also
reduce the number of true Increase and
Decrease calls (decreases sensitivity).
Increasing γ2L and γ2H increases γ2.
Increasing γ2 may reduce the number of
false No Change calls (increases
specificity) and may also reduce the
number of true No Change calls
(decreases sensitivity).
Increasing d may increase the number of
true No Change calls (increases
sensitivity) and may also increase the
number of false No Change calls
(decreases specificity).
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679
Changing a Parameter Value
In the Parameters tab and make a selection from the Probe Array
Type drop-down list.
2. Click the parameter you wish to change.
The parameter box displays the current value (Figure F.45).
1.
Figure F.45
Expression Analysis Settings, Parameters tab
Enter a new value for the parameter in the parameter box.
4. Click OK to close the Expression Analysis Settings dialog box.
3.
Cell Summary Report Algorithm
The Cell Summary report algorithm is useful in identifying gridding,
scanning, and library file issues.
The Cell Summary report uses the control features on the chip. Control
features are cells with special probes; the corresponding targets are
spiked into the sample cocktail. The resulting patterns of bright and
dark cells are used in grid alignment and other processes.
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Different algorithms are used for:
• Expression, Genotyping and other non-resequencing chips (see
below)
• Resequencing chips (see page 679)
The algorithm input files are:
• .GRC files available on the library CD or the Affymetrix web site.
• Image CEL files.
Algorithm for Non-Resequencing Chips
For non-resequencing chips (expression, genotyping, and others), the
algorithm uses three types of features for image data evaluation:
• OligioB2
• OligoB1
• NonSynthesized
Refer to the relevant manual for the GeneChip array for more
information about these features.
For an ideal experiment:
• The nonsynthesized features would have dim intensities.
• One of the feature types (either the oligoB2 OR oligoB1) would
be bright because it was spiked into the sample cocktail.
• The other feature type (oligoB2 OR oligoB1) would be dim
because it was NOT spiked into the sample cocktail.
The algorithm uses the following steps:
1.
The algorithm determines whether the OligioB1 or OligoB2 is
overall brighter for this image (the cell file) using the medians of
the OligoB1 vs. OligoB2 features.
2.
A dim threshold and a bright threshold are determined based on
the medians described above. The threshold is the midpoint
between the logarithms of the medians.
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681
3.
Features whose intensity is beyond the thresholds are flagged as
having unusual brightness (or dimness). These features are
observed due to:
- Misaligned grid
- Debris
- Probe death
4.
The flagged cells can be masked from the image using the cell
summary options. When the image data is opened the flagged cells
are visible as masked out data.
The cell summary report is saved with a suffix of
“_cell_summary.rpt.” The data in the output file is described in
The Cell Summary Report, on page 178.
Algorithm for Resequencing Chips
For Resequencing chips, the algorithm uses three types of features for
image data evaluation:
• Non-synthesized features.
• OligoB2 checker features (oligoB2 features arranged in a
checkerboard pattern).
• OligoB2 Extended features (oligoB2 features arranged in a
Resequencing pattern).
Refer to the relevant manual for the GeneChip array for more
information about these features.
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Appendix
G
GCOS Data Types
Appendix
G
685
GCOS Data Types
Probe Information (Library) Data
The probe information or library data includes the probe array design
characteristics, probe utilization and content, and scanning and
analysis parameters. Library data are unique to each probe array type.
Library data includes user-defined mask files (see Table G.1). The
default path for the library directory is
<servername>:\GeneChip\Affy_Data\Library.
Table G.1
User-defined mask files
Mask File Name
File
Extension
Description
Probe Mask
.msk
A user-specified list of probe pairs that
are excluded from an analysis.
Cross Hybridization
Probe Mask
.msk
A type of probe mask that specifies probe
pairs that include a PM or MM probe cell
whose intensity exceeds a user-specified
limit. These probe pairs will be excluded
from the analysis.
Hybridization Probe
Mask
.msk
A type of probe mask that specifies probe
pairs where PM – MM < Difference
Threshold or PM/MM < Ratio Threshold.
These probe pairs will be excluded from
the analysis.
Spike Probe Mask
.msk
A type of probe mask that specifies probe
pairs where:
(PM – MM)spike – (PM – MM)unspike <
Difference Threshold or (PM-MM)spike/
(PM – MM)unspike < 1 + Ratio Threshold.
These probe pairs will be excluded from
the analysis.
Fluidics Protocol Data
The fluidics protocol data include the instrument control instructions
used by the GeneChip® fluidics station. Fluidics protocols are written
to a directory that is specified during GCOS installation. The default
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path for the fluidics protocols is
<servername>:\GeneChip\Affy_Data\Protocol.
Experiment Data
During experiment setup, you enter information to register the
sample and define the experiment. The software generates the other
experiment data (image, cell intensities, probe analysis data) as the
analysis proceeds. Experiment data are written to a directory that is
specified during GCOS installation. The default path for experiment
data is <servername>:\GeneChip\Affy_Data\Data\.
GCOS stores the experiment data in the process database, a relational
database that maintains associations between experiments, samples,
and the experiment data generated during analysis. Table G.2 explains
the different types of experiment data in the process database.
Table G.2
Experiment data files
Experiment
Data Name
Data Description
Experiment
Information about the experiment name, sample, and probe
array type. The experiment name also provides the default
name for subsequent data that are generated during
experiment analysis.
Image Data
Image of the scanned probe array (.dat file) and information
about the experiment & sample that the image pertains to.
Cell Intensities
Single intensity value for each probe cell delineated by the
grid (.cel file calculated by the Cell Analysis algorithm) and
information about the: 1) image that the cell intensities were
derived from, and 2) experiment and sample that the image
pertains to.
Probe Analysis
(chip data)
Output generated from the analysis of a probe array (.chp
file) and information about the: 1) cell intensities for the
analysis, 2) image that the cell intensities were derived
from, and 3) experiment and sample that the image pertains
to.
appendix G | GCOS Data Types
687
Table G.2
Experiment data files
Experiment
Data Name
Data Description
Report
Report generated from the analysis output file (.chp) and
information about the: 1) analysis output file (.chp) the
report was derived from, 2) cell intensities for the analysis,
3) image that the cell intensities were derived from, and 4)
experiment and sample that the image pertains to
Data
A standard format for text files. GCOS exports text in this file
format.
A standard format for Excel files. GCOS export text in this
file format.
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Appendix
H
Base Codes and Amino Acid
Abbreviations
Appendix
H
691
Base Codes and Amino Acid
Abbreviations
IUPAC Base Codes
Table H.1
Base Codes
IUPAC Code
Group
Base(s)
A
A
Adenine
C
C
Cytosine
G
G
Guanine
T
T
Thymine
M
A or C
aMino
R
A or G
puRine
W
A or T (U)
Weak interaction (2 H bonds)
Y
C or T (U)
pYrimidine
S
C or G
Strong interaction (3 H bonds)
K
G or T(U)
Keto
V
A or C or G
not-T or not-U (since V follows
U)
H
A or C or T(U)
not-G (since H follows G)
D
A or G or T(U)
not-C (since D follows C)
B
C or G or T(U)
not-A (since B follows A)
N
A, C, G or T(U)
aNy
Amino Acid Abbreviations
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Table H.2
Amino acid abbreviations
One Letter
Three Letter
Amino Acid
A
Ala
Alanine
B
Asx
Asparagine or Aspartic acid
C
Cys
Cysteine
D
Asp
Aspartic acid
E
Glu
Glutamic acid
F
Phe
Phenylalanine
G
Gly
Glycine
H
Hi
Histidine
I
Ile
Isoleucine
K
Lys
Lysine
L
Leu
Leucine
M
Met
Methionine
N
Asn
Asparagine
P
Pro
Proline
Q
Gln
Glutamine
R
Arg
Arginine
S
Ser
Serine
T
Thr
Threonine
V
Val
Valine
W
Trp
Tryptophan
Y
Tyr
Tyrosine
Z
Glx
Glutamine or Glutamic acid
Appendix
I
Toolbars, Hot Keys, & Windowpanes
Appendix
I
695
Toolbars, Hot Keys, & Windowpanes
This appendix reviews toolbar button functions, hot keys, and explains
how to resize windowpanes or columns.
This appendix contains the following sections:
• Toolbars (see below)
• Hot Keys (see page 702)
• Working with Windowpanes & Columns (see page 705)
• Resizing or Hiding Columns in the EAW (see page 706)
Toolbars
You can display toolbars with text labels (Figure I.1). To display the
toolbar button labels, select View → Toolbar → Text Labels from
the menu bar.
GCOS TOOLBARS
Main Toolbar
Figure I.1
Main toolbar
Table I.1
Main toolbar
Menu Bar Command
File → Open
File → Save
Toolbar
Button
Function
Displays the Open dialog box so that data (for example, probe
analysis data or image data) may be opened.
Saves the open image, experiment, or report.
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Table I.1
Main toolbar
Menu Bar Command
Toolbar
Button
Function
File → Print
Displays the Print dialog box.
Window → Data Tree
Displays or hides the data tree.
Window → Shortcut Bar
Displays or hides the shortcut bar.
Window → Status Log
Displays or hides the status log.
Run → Experiment Info
Displays experiment window.
Run → Fluidics
Displays the Station Selection dialog box for the Affymetrix®
Fluidics Station 250/450.
Run → Scanner
Displays the Scanner dialog box.
Run → Stop Scanner
Stops a scan in progress.
Run → Analysis
Runs an analysis on the open *.dat or *.cel data.
Edit → Image Settings
Displays the Image Settings dialog box.
Help → Contents
Displays GCOS help.
Expression Analysis Window (EAW) Toolbar
Figure I.2
EAW toolbar
appendix I | Toolbars, Hot Keys, & Windowpanes
697
Table I.2
EAW toolbar button functions
Menu Bar Command
EAW
Toolbar
Button
Function
Edit → Find
Displays the Find Probe Set dialog box.
Edit → Sort
Displays the Sort dialog box.
View → Hide Selected
Hides selected probe set(s) in the metrics or pivot table.
View → Hide Unselected
Hides unselected probe set(s) in the metrics or pivot table.
View → Unhide All
Displays all probe sets previously hidden in the metrics or pivot
table.
Analysis → Options
Displays the Analysis Options dialog box.
Graph → Clear Selected
Graphs
Clears selected graphs from the graph pane in the EAW.
Graph → Scatter
Correlation Graph
Displays the Scatter Graph dialog box.
Graph → Series Graph
Displays the Select Series Graph Parameter dialog box.
Graph → Intensity Bar
Graph
Plots the Intensity Bar Graph for the selected probe set(s).
Graph → Measured
Images
Displays the hybridization intensity image data (.dat) for the
selected probe set(s).
Graph → Lasso Points
Changes the cursor to a drawing tool that enables the user to draw
a circle around points in a scatter graph.
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Batch Analysis Toolbar
Figure I.3
Batch analysis toolbar
Table I.3
Batch analysis toolbar button functions
Menu Bar
Command
Edit → Add Item
Edit → Remove Item
Batch Analysis
Toolbar
Button
Function
Displays the Open dialog box to select and add *.cel files to
the Batch Analysis window.
Removes the selected *.cel files from the Batch Analysis
window.
Edit → Start Analysis
Starts the batch analysis.
Edit → Stop Analysis
Stops the batch analysis.
View → Options
Displays the Batch Analysis Options dialog box.
Report Toolbar
Figure I.4
Report window toolbar
appendix I | Toolbars, Hot Keys, & Windowpanes
Table I.4
Report toolbar button functions
Menu Bar
Command
Report
Toolbar
Button
Edit → Cut
Function
Removes a highlighted selection from the report.
Edit → Copy
Copies a highlighted selection in the report to the system
clipboard.
Edit → Paste
Pastes a copied or cut selection at the current insertion point.
Edit → Find
Displays the Find dialog box.
Edit → Find Next
Performs a text search for the item specified in the Find dialog
box.
Publish Toolbar
Figure I.5
Publish window toolbar
Table I.5
Publish toolbar button functions
Menu Bar
Command
Publish
Window
Toolbar Button
Function
Publish → Add
Item
Displays the Open dialog box to select and add experiment data
(task items) to the publish task.
Publish →
Remove Item
Removes the selected task item(s) from the publish task.
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Table I.5
Publish toolbar button functions
Menu Bar
Command
Publish
Window
Toolbar Button
Function
Publish →
Publish
Send the task to the GCOS server to be published during the
time specified by the GCOS Server administrator.
Publish →
Monitor →
Cancel Publish
Cancels a task (changes the task status from WAIT to
CANCELED).
Publish →
Monitor →
Restart Publish
Reinstates a canceled task to be published during the time
specified by the GCOS Server administrator (changes the task
status from CANCELED to WAIT).
GCOS MANAGER TOOLBAR
Figure I.6
GCOS Manager toolbar
Table I.6
GCOS Manager toolbar button functions
Menu Bar
Command
GCOS Manager
Toolbar Button
Function
Process → Print
Experiment
Prints experiment information.
Tools → Register
GCOS Server
Opens the Register GCOS Server dialog box
Tools → Server
Event Viewer
Opens the Server Event Viewer
appendix I | Toolbars, Hot Keys, & Windowpanes
Table I.6
GCOS Manager toolbar button functions
Menu Bar
Command
GCOS Manager
Toolbar Button
Function
Tools → Server
Tasks
Displays the Task List for the active server.
Tools → File Path
Displays the Select Export File Path dialog box
Tools → Find
Opens the Find dialog box
Tools → Filter
Opens the Sample Filters dialog box
Tools → Help
Topics
Opens GCOS Manager online help.
GCOS ADMINISTRATOR TOOLBAR & ICONS
Figure I.7
GCOS Administrator toolbar
Table I.7
GCOS Administrator toolbar button functions
Menu Bar
Command
GCOS
Administrator
Toolbar Button
Function
Opens the Administrator Password dialog box so that a system
administrator password or publish database password can be
created and updated.
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Table I.7
GCOS Administrator toolbar button functions
Menu Bar
Command
GCOS
Administrator
Toolbar Button
Function
Refreshes the data tree in the copy or space management view.
Refresh the data tree to view new data or databases added to
the system during the current session.
Tools → Register
GCOS Server
Opens the Register GCOS Server box.
Tools → Server
Tasks
Opens the Sample Filters dialog box.
Tools → Help
Topics
Opens GCOS Manager online help.
Table I.8
GCOS Administrator Icons
Process Database or
LIMS System Database
(yellow)
Project
Sample
Publish Database
(gray)
Experiment
Information
Filter
Hot Keys
appendix I | Toolbars, Hot Keys, & Windowpanes
Table I.9
GCOS hot key descriptions
Menu Bar Command
Hot Key
File → Open
Ctrl + O
File → Print
Ctrl + P
Edit → Copy
Ctrl + C
File → Save
Ctrl + S
Edit → Image Settings
S
Edit → Delete
Del
Edit → Unmask All Cells
Shift + U
View → Grid
G
View → Probe Cell Data
C
View → Corner → Upper
Left
F5
View → Corner → Upper
Right
F6
View → Corner → Lower
Left
F7
View → Corner → Lower
Right
F8
View → Image → Measured M
View → Image → Difference D
View → Image → Average
A
View → Next Highlight
N
View → Previous Highlight
P
View → Clear Highlights
E
View → Probe Tiling
T
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Table I.9
GCOS hot key descriptions
Menu Bar Command
Hot Key
1, 2, 3, etc.
(toggle between open image windows)
I
(Image window zoom in)
Select an area in the image window with
the cursor and press I
(Zooms in on the selected area)
O
(Image window zoom out)
Shift+O
(Image window full zoom out)
L
(intensity autoscale)
Edit → Mask Cells
X
Edit → Unmask Cells
U
Help
F1
Scroll up one page
Page Up
Scroll down one page
Page Down
Scroll left one page
Ctrl + Page Up
Scroll right one page
Ctrl + Page Down
Scroll up 1/10 page
Up arrow
Scroll down 1/10 page
Down arrow
Scroll left 1/10 page
Left arrow
Scroll right 1/10 page
Right arrow
appendix I | Toolbars, Hot Keys, & Windowpanes
Table I.10
GCOS Manager hot key descriptions
Menu Bar Command
Hot Key
View → Refresh
F5
Working with Windowpanes & Columns
You can resize windowpanes.
1.
Place the mouse pointer over a windowpane border so that it
changes to a double arrow
(Figure I.8).
Figure I.8
Resize windowpanes horizontally or vertically
2.
Drag the border to resize the windowpane.
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Resizing or Hiding Columns in the EAW
You can resize or hide columns in the Expression Analysis window
(EAW). GCOS stores the column settings for future sessions on a per
user basis (identified by the logon name) so that one user’s settings do
not affect the settings of another.
Position the mouse over the left or right cell border in the column
header so that it changes to a double arrow
.
2. Drag the cell border to resize the width of the column.
3. To hide a column, drag the left or right cell border of the column
header until the column width is reduced to zero; or
Right-click the column header in the EAW and select Hide
Column from the shortcut menu that appears.
1.
Appendix
J
Database Management & Data Source
Name Descriptions
Appendix
J
709
Database Management & Data Source
Name Descriptions
This appendix contains the following sections:
• Performance Tuning for SQL Server Databases (see below)
• Client Tuning (see page 711)
Performance Tuning for SQL Server
Databases
Microsoft® SQL Server automatically tunes many of the server
configuration options, therefore requiring little, if any, tuning by a
database administrator. Although these configuration options can be
modified by the database administrator, it is generally recommended
that they are left at their default values, allowing SQL Server to
automatically tune itself based on run-time conditions.
However, if necessary, the following components can be configured to
optimize server performance:
• SQL Server Memory
• I/O subsystem
• Microsoft® Windows® options
To improve performance of querying, it is recommended that the SQL
Server database is in three devices: data, index and log. With this
separation, reading and writing of data is improved which helps
decrease amount of time it takes to query data.
DATA DEVICE
The data device stores the experimental data, published data, and
other data associated with GCOS. These data are accessed by GCOS
and all applications that work on GCOS. The name of this device is
<publish database name>_DAT.mdf.
To move the locations of data devices from one disk to another, use
the Space Manager tool in GCOS Administrator.
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To improve performance, the Data Device file should be placed on a
dedicated physical disk.
INDEX DEVICE
The Index Device is available for publish databases. The Index Device
provides quick access to data and can enforce uniqueness on the rows
in a table. With this device, it allows searches in a database program
to find data in a table without scanning the entire table. This device is
a list of values in a table with the storage locations of rows in the table
that contain a value. The name of this device is
<publish database name>_INDEX_mdf.
To move the locations of data devices from one disk to another, use
the Space Manager tool in GCOS Administrator.
Basic Configuration
The index files can be located with the Data Device files, however,
performance may be gained by placing the Index Device file on a
different disk with low activity.
Advanced Configuration
Place the Index Device file on a dedicated physical disk. If a remote
AADM server is used, place the Data Device file on a dedicated
physical disk.
LOG DEVICE
The Log Device holds the information used to recover the database.
There must be at least one log file for each database.
To move the locations of log devices from one disk to another, use
the Space Manager tool in GCOS Administrator.
appendix J | Database Management & Data Source Name Descriptions
711
Basic Configuration
The Log Device file can be placed where there is space.
Advanced Configuration
Place the Log Device file on a dedicated physical disk.
If a remote AADM server is used, place the Data Device file on a
dedicated physical disk.
ADDITIONAL PERFORMANCE TUNING INFORMATION
These are other suggestions that can help improve the performance of
your system.
• Separate all devices SQL Server uses. For example, place the data
device, index device, and log device each on their own individual
physical disk. The separation of these files improves the
performance by allowing the drive heads to perform read only or
write only operations during the majority of the publishing
operation.
• Use a remote AADM server for publishing and place the data
device, index device, and log device each on their own individual
physical disk.
• Placing both the index device and log device on the same disk can
slow performance since there is a lot of read and write activity
being performed.
Client Tuning
As part of the software requirement for the client, it is recommended
to install SQL*Loader on the client running Data Mining Tool if
connecting to an Oracle® GCOS server. Also, a registry setting can be
added on the client machine when preforming a large pivot.
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SQL*LOADER
If your GCOS server uses an Oracle® database, it is advisable to install
SQL*Loader on the client workstation. Contact your Database
Administrator to install SQL*Loader. SQL*Loader is included on the
Oracle® installation CD.
SQL*Loader is used to bulk loading probe set lists and annotations
that users save into the database. With SQL*Loader installed on the
client, the process of saving large amounts of data at time is improved.
Without SQL*Loader installed on the client, it may take a long time
to save the information.
The same version of SQL*Loader must be installed on the
workstation as on the GCOS server.
Appendix
K
Troubleshooting
Appendix
K
715
Troubleshooting
This section of the manual helps you troubleshoot problems that may
be encountered during installation or administration of the server and
the different software products on the clients.
This will also help you with some basic troubleshooting techniques
and what information should be gathered to help Technical Support
work towards providing a resolution to a potential problem that you
are experiencing.
This appendix contains the following sections:
• Troubleshooting Questions (see below)
• GCOS 1.4 Troubleshooting (see page 716)
• GCOS Manager 1.4 Troubleshooting (see page 721)
• Library Files Troubleshooting (see page 727)
Troubleshooting Questions
Some basic tests may quickly reveal the cause of the problems. It is
important to isolate the problem down to a particular area. Some
questions to answer before calling Technical Support for help:
Is it a client or a server problem?
If server, has anything changed? Addition of software? Addition of
network functions? Restoring of databases?
Check the Event log.
Check the SQL Server log (if using a Microsoft® SQL Server database).
Which database is being accessed?
Is there enough free space available?
Can you reproduce the problem? What steps were taken?
What is the exact error message?
Does it happen with a particular user or all users?
What has changed on the client?
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Is the user logged onto the correct domain? Does the user have
permissions to access GCOS Server?
Can you write to the publish database?
Can you access other databases?
Can you reproduce the problem? What steps were taken?
What is the exact error message?
GCOS 1.4 Troubleshooting
This section provides tips on troubleshooting problems in the
following GCOS features:
• Installation (see below)
• Installing Pre-GCOS Version Libraries (LIMS 3.0 Libraries) on the
Client (see page 717)
• Publishing (see page 718)
• Licensing (see page 720)
• Workflow (see page 720)
INSTALLATION
• I am unable to install the software.
Verify that you have administrative privileges in order to install
the software.
• Error connecting to GCOS Server database.
Check the connectivity. Check the server is running.
• When installing GCOS 1.4 the installation tries to copy files,
however, the error message “cannot move error - 145”
appears. What should I do?
Verify that all Affymetrix applications are closed and not running.
Log in as another user and, again, try installing the application. It
may be the user’s profile is corrupted.
appendix K | Troubleshooting
717
• The GCOS software shows the following dialog box when
installing the software or MSDE fails to install.
Figure K.1
Stop message
GCOS requires MSDE. In order to install MSDE, the “Server”
service also known as the “lanmanmanger” service needs to be
installed and running. GCOS will attempt to start the service if it
has stopped.
To see if the “Server” service is installed, right-click “My
Computer” and select “Manage”. Navigate to the “Services and
Applications” Node”. Select Services and see if the Server service is
installed.
To install the Server service the workstation must have a Network
Interface Card (NIC) or a Microsoft loop-back adapter. Once the
NIC has been installed, the “Server” service can be installed by
adding the “File and Printer Sharing for Microsoft Networks” to
the Local Area Connection properties. Refer to
www.microsoft.com or contact your system administrator for
details on installing the server service.
INSTALLING PRE-GCOS VERSION LIBRARIES (LIMS 3.0 LIBRARIES) ON THE
CLIENT
In order to install LIMS 3.0 version libraries (pre-June 2003 libraries)
on a GCOS client, you must complete the following four steps.
1.
Run ToggleLIMS3LibrarySupport.exe file by double-clicking the
file. (The ToggleLIMS3LibrarySupport.exe file is located in the
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directory where GOCS was installed.) This enables the older
library installer and temporarily disables GCOS.
2. Install the old version library.
3. Run the ToggleLIMS3LibrarySupport.exe file by double-clicking
the file again. This enables GCOS and disables the old library
installer. GCOS cannot be run until this step is completed.
4.
Run the library migrate program (from the subdirectory 'Migrate'
contained in the GCOS Target directory, or a new version library
install CD).
PUBLISHING
• Unable to publish data. The server task window displays
that it is in the queue and says “wait”.
Verify that the publishing service is active in the server task
window of GCOS 1.4. If the service is stopped, contact the system
administrator to start the gcdoservice.
• GCOS shows “Publishing Stopped” when a publish window
is launched.
Check if CGCDOService is started.
• Unable to publish the .chp file. The user is able to publish
any .exp and .cel files, however, when publishing the .chp
file, the error message “Failed to publish x.chp: SQL
Command Failure.”
This is possibly due to a probe array type that has been installed
and published. However, a new probe array with the same name
containing new probe information was installed. The probe set
names were changed and therefore do not match and that is why
the .chp file with the new probe array information cannot be
published.
Workaround: Delete the data that is published from that probe
array type. Reanalyze that existing .chp files and publish again.
• Unable to Publish to an Oracle® GCOS Server system and
the Oracle® Publish database was created successfully.
appendix K | Troubleshooting
719
Check the registry setting: HKLM\Software\ODBC\ODBC.INI
on the GCOS server.
Locate the Oracle ODBC DSN created
<servername>_ORCL_GATC.
Verify the values:
String Value Name
HOST_OS
HOST_SQLLOAD
Oracle® 8.1.7
Value
WinNT4
sqlldr
Note: String values are case-sensitive
For the Publish database: <publish database name>_AffyPub:
String Value Name
Value
PWD
<encrypted password>
UID
<publish database name>
Alias
<name of the alias>
Note: The name of the alias created points to the GATC publish server
Do the temporary files get created? *.ctl on the root of the c: drive
for the Oracle database.
The temporary files on the c:\ drive for SQL Server are s*.* (short
file names).
There must be enough free space to create these temporary files (at
least 400MB).
• “Failed to read <name of experiment> from GCOS Server
for the .dat file” message appears when publishing.
There is no .dat file. The experiment needs to be scanned and is
currently in the scan stage.
• “Failed to read <name of experiment> from GCOS Server
for Chip.” message appears when publishing.
There is no object file. The experiment is currently in the
hybridization queue and needs to be hybridized and scanned.
Publish Task Queue should be purged from time to time. As the
task queue grows, especially above 10,000 entries, GCOS will
appear to hang temporarily when placing jobs in the publish
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queue. You may want to backup the text of this log prior to
purging.
LICENSING
• Upon Launching GCOS 1.4, the license window appears. I
enter the license, however the window keeps appearing.
Verify that when entering the license, the license number is
entered exactly as seen. The license is case sensitive. Ensure that
you do not enter any additional spaces.
WORKFLOW
• Failure in GetSampleBy name command error.
Verify that you did not enter any illegal characters used when
creating a sample or experiment. Some illegal characters include:
< >:;\”^|*/?
• Cannot connect to Affymetrix GCOS Server.
Verify that the network is up. Also, verify that the server is online.
On the client side, verify that the registry key values are correct.
• Experiments don't show up in the data tree.
Verify your filter is not filtering out everything, especially the date
range.
• When trying to reanalyze an analysis after an upgrade in
GCOS, the error message “Base call failed for
\\<servername>\gcgcosserver\data\\<file.chp> - Invalid base
call algorithm. Verify base call default settings for this Probe
Array Type or verify Tools\Defaults\File locations settings”
appears.
One indication of this error message is that the library file update
on the server may not have updated properly.
appendix K | Troubleshooting
721
GCOS Manager 1.4 Troubleshooting
This section provides tips on troubleshooting problems in the
following GCOS Manager features:
• Installation (see below)
• Delete (see page 722)
• Archiving (see page 722)
• Importing (see page 723)
• Usersets (see page 723)
• Templates (see page 724)
• Exporting (see page 724)
• Publish (see page 724)
• GCOS Manager FAQs (see page 725)
INSTALLATION
• When trying to register a GCOS server or click a tab in
GCOS Manager, the error message “GCOS Server
Component not installed” appears. What does this mean?
This means that there is a permission or access problem, or may
occur where the shared pool size is too small.
Verify that the user has permissions to access the server. The logon
name is part of the GCOS Server Global Group.
Verify that the user is registering a server with the GCOS Server
components installed.
Verify that the database services are started (either SQL or
Oracle®).
• The Roles tab in GCOS Manager is missing.
The Roles tab is unavailable when you work with GCOS connected
to the local MSDE database server.
The global group may have the wrong domain name prefix in the
GCOS Server Admin database table 'USERS'. This will happen if
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your MIS changes the name of the domain. As users begin to
migrate to Win2K from NT, some administrators might change
the domain name. If they do, you will need to change the domain
name in the 'USERS' table.
• Slow connection when trying to connect to the server with
one of the client applications (i.e.: GCOS Manager). What is
going on?
If users experience slow connection to the server, verify that the
Domain Controller and DNS are properly configured and
registered with other Domain Controllers within the network.
DELETE
• Unable to delete data from the process database.
Verify the error message. Error message displayed “Failed to read
experiment: xxx.EXP” It is possible that the data was migrated in
from a beta version and the character limit exceeded 25 characters.
In this case, the entire sample must be deleted in order to remove
the file in question.
• When trying to delete data from a Publish database, it
displays “failed” When viewing the log, the message
“IpublishData – Failure in CheckForOpenConnections:
cannot delete database with open connections (2)” What
does this mean?
If another user has the database open (using DMT or publishing
data), data cannot be deleted. This is because the tables are locked
and cannot be accessed. Wait until the users are done publishing
and not using DMT.
ARCHIVING
• Unable to archive. Error message “Archive File Copy Error”.
Verify that the path location specified for archiving has enough
free space to archive the file(s) selected.
appendix K | Troubleshooting
723
IMPORTING
• Unable to import. I get a copy file error message in the text
log.
Verify that the permissions are set properly.
There is enough free space to import the files.
If the data is on a CD, try copying it to the local hard drive and
import again.
• Trying to import and the error message “Cannot modify
experiment <name of experiment>. It is waiting to be
hybridized, scanned, or it’s image file requires grid
alignment.”
The experiment that is selected to be imported cannot be imported
because this experiment is already on the queue and is waiting to
be completed by one of the above steps.
• Trying to import data and it fails. Verify that the .exp and
.dat files exist with the same name.
Verify that the files are a valid size. If the data is on a jaz disk, CDROM, or other media, try copying it to the local hard drive and
import again.
USERSETS
• In GCOS Manager, the user is unable to create a userset.
Verify that the information entered is correct.
Verify that the userset parameters are valid in GCOS Manager.
Verify that the library files have been installed or updated.
• In GCOS Manager, I click the Usersets tab and get the
message “Failed to load probe arrays -?|”
This means that there have not been any probe arrays (library files)
installed.
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TEMPLATES
• Unable to create a template.
Verify that there is not any other template with the same name.
Verify that the template was saved.
EXPORTING
• Unable to export. Error message “CopyFile Error=112”.
Verify that the path location specified for exporting has enough
free space to write the .exp, .dat, .cel and .chp files.
PUBLISH
• Unable to create new Publish database.
Verify that the username and password entered are correct.
Verify that the path location specified exists.
Verify that the path location specified has enough hard disk space.
Verify that the open cursors set to 200 (Oracle databases only).
Verify that the publish database name does not start with a
number. All publish databases and database passwords must begin
with a letter.
• Creating a SQL Server Publish database. The error message
“Device too small” or “Device too large” is displayed. What
should the creation size be?
The size of creating the publish database is between 128 MB and
1024 MB.
• Trying to create an Oracle® publish database and it fails.
Verify that the username and password entered is correct. The
password for the username gatc is ‘gatc’ (all lowercase). Verify that
the path exists. Verify that the open cursors is set to 200. Verify
there is enough hard disk space.
• Creating an Oracle® database and it fails. The log shows that
there are not enough cursors. What does this mean?
appendix K | Troubleshooting
725
Verify that the INIT.ORA contains the open_cursors =200 (It
needs enough cursors to create a database, otherwise all cursors are
locked and in use).
• Unable to delete Publish data from the publish AADM
database.
The publish data selected to be deleted may be in use by another
user. Other users may have the Data Mining Tool application open
and connected to that publish AADM database. Therefore, in order
to delete the data, the other user must exit out of DMT.
• After removing a publish database from the database
application, the database name still appears in the publish
tab. Why?
The system DSN still exists in the ODBC Control Panel. Remove
the DSN and it will not appear in the application.
GCOS MANAGER FAQS
This section of the manual lists frequently asked questions (FAQs)
regarding Affymetrix GCOS Manager. If you still need assistance after
reviewing these questions and answers, please contact Affymetrix
Technical Support. For support contact information, see Technical
Support, on page 6.
Q:
I want to view information about other expression samples. I try to select another
sample by clicking its icon, but the software doesn’t change to a different sample.
What should I do?
A:
In GCOS Manager, click the text representing the sample or experiment name
rather than the icon.
Q:
How can I change the “export to” or “import from” location?
A:
On the menu bar, click the
icon. If you are in the Process, Publish, or
Find tabs, this will select a target location for exported files. If you are in the
Import tab, this will select a location to import files.
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Affymetrix® GeneChip® Operating Software User’s Guide
Q:
How do I use the Find command to search the Publish database?
A:
The Find command only works with the Process database.
Q:
I know some of my samples (projects or experiments) are in the process database.
However, when I use the Find command, the results produce an empty set. Why
does this happen?
A:
In the Find window, the Select Object tab, the Advanced Filter tab, and the Data
Filter tab are additive. Therefore, if you select experiments with the text string
“xxxAssay” using the Select Object tab and then limit the search to Project X using
the Advanced Filter tab, the Find command searches for experiments with the
text string “xxxx” that are members of Project X.
Q:
I want to delete (assume ownership, export, or archive) multiple data items
(experiments or samples) at one time. However I cannot select multiple data items
at one time in the process database. How can I accomplish this?
A:
You can SHIFT-select or Ctrl-select multiple data items at one time in the Find
window. Most of the functions that are available in the Process tab are also
available in the Find window.
Q:
I want to archive a sample but the software will not let me choose that function.
How do I archive a sample?
A:
Experiments or samples cannot be archived. A list of available functions in the
Find window is listed below:
Analysis data: archive, assume ownership, delete, and export
Experiments: assume ownership, delete, export, and rename
Samples: assume ownership, delete, and rename
Q:
How do I get out of the Find window and back to the process database?
A:
Simply close Find window or go to the Microsoft® Windows® menu and select
“GCOS server manager.”
Q:
Can I view property information about files in the publish database?
A:
No, this information is not available. But you can view property information
about files in the process database in the Publish or Process tab.
appendix K | Troubleshooting
727
Q:
I cannot find my image data (.dat) under the Import tab. I have confirmed that the
.dat file exists on the local drive and that I have the import location mapped
correctly. Why doesn't GCOS Manager let me import my image data (.dat)?
A:
GCOS Manager imports .exp data and the associated image data (.dat) with the
same name. Make certain that the folder with the image data (.dat) includes the
.exp data with the same name. As a last resort, open the image data (.dat) in
Affymetrix® GCOS. If an .exp does not exist for the image data (.dat), GCOS
will automatically create one.
Q:
When I try to open a Sample folder, only a few samples are displayed and I know
that there should be more in the database. What happened to the samples?
A:
The Sample filter remains active during successive sessions. Reset Sample Filter
parameters. See Filtering Data, on page 71.
Library Files Troubleshooting
INSTALLATION
• During the library file installation on the server, it shows
that the ask is “not responding” in task manager. What is
wrong?
The library file installation is responding. During this time, it is
writing the gene descriptions and sequence information into the
databases. This will take a while depending on the number of
probe arrays selected. Do not stop or cancel the task.
• After an upgrade, the library files update installation is run.
The installation completes very fast. Is this correct?
Yes. The update copies the *.cif file in the
X:\GeneChipDB\Library directory and adds new parameters to the
database. Descriptions and sequences are not installed.
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Appendix
L
Using the GeneChip® AutoLoader
Appendix
L
731
Using the GeneChip® AutoLoader
The GeneChip® Autoloader is a new addition to the GeneChip®
Scanner 3000, designed expressly for scanning multiple GeneChip®
probe arrays. The Autoloader can scan up to 48 probe arrays
automatically without operator presence.
Figure L.1
The Affymetrix® GeneChip® Scanner 3000 with AutoLoader
This appendix contains the following sections:
• Setting Up the AutoLoader (see below)
• Installing and Configuring the E-mail System (see page 739)
• Operating the Scanner-AutoLoader (see page 746)
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• Quick Reference Walkthrough (see page 747)
• The AutoLoader Run (see page 751)
• Cleaning and Maintenance (see page 787)
• Troubleshooting (see page 787)
• GeneChip® Scanner 3000 - AutoLoader Specifications (see page 794)
• CE Mark Declaration of Conformity (see page 795)
• Regulatory (see page 796)
Setting Up the AutoLoader
The GeneChip® Scanner 3000 with an AutoLoader has the following
connections on the unit (Figure L.3):
• AC power connection
• Ethernet connection
• Keyboard/barcode reader connection
If you must move the scanner, disconnect all cables first.
• The instrument weight is approximately 100 pounds (45.36 Kg).
Do not place it on an unstable cart, stand, or table. Failure to
properly support the instrument may cause serious damage or
injury and may void the warranty.
Heavy object. Two people are required to lift the scannerAutoLoader.
See the following sections for more information on setting up the
Autoloader:
• Connecting the Scanner and Workstation (see below)
• Indicator Lights and On/Off Button (see page 737)
appendix L | Using the GeneChip® AutoLoader
733
CONNECTING THE SCANNER AND WORKSTATION
1.
Couple the barcode reader to the keyboard using the coupling
block (Figure L.2). Connect the coupling block to the
workstation’s keyboard port (Figure L.3).
Cable to
Keyboard
Cable to
Barcode
Reader
Cable to
Workstation
Keyboard
Receptacle
Barcode readerKeyboard
Coupling Block
Figure L.2
Coupling the barcode reader to the keyboard
Connect the 3-pronged electric power plug to the workstation
(Figure L.3).
3. Connect the dedicated Ethernet cable from the scanner to the
Ethernet port that is designated on the workstation. The port is
located near the bottom of the workstation (Figure L.3).
4. You can connect your company’s network cable to the indicated
port near the center of the workstation (Figure L.3).
When you start GCOS, the software will make the proper
communication connections.
5. Connect the cabling to the scanner with AutoLoader (Figure L.4)
2.
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Affymetrix® GeneChip® Operating Software User’s Guide
Do not confuse your company’s network connections with the
dedicated Ethernet port of the scanner-workstation. The proper
scanner connection is located near the bottom of the workstation.
This 10/100 Base T Ethernet communications port is dedicated to
the scanner-workstation interface. You cannot connect the scanner
to your company’s Ethernet communications network.
You can, however, connect the workstation’s second Ethernet port
to the your company’s Ethernet network.
6.
On the rear of the AutoLoader, there are two drain tubes: an upper
and a lower drain tube. Place the upper drain tube in a beaker or
other receptacle to collect the condensation from the AutoLoader
(Figure L.4).
The reset button is the scanner’s circuit breaker. The breaker switch
will be tripped whenever the scanner experiences an electrical fault
condition. Press to reset. If you cannot reset this switch, contact
Affymetrix technical support.
appendix L | Using the GeneChip® AutoLoader
3-Pronged
Electric
Power
Plug
KeyboardBarcode
Coupler
Block
Network
Connection
Barcode
Reader
Connection
Keyboard
Cable
AutoLoader
Connection
Figure L.3
Workstation rear cable connections
735
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Affymetrix® GeneChip® Operating Software User’s Guide
Circuit
Breaker
Reset
Button
Cable
Receptac
to Works
Power
Cable
Upper
Drain
Tube
Lower
Drain
Tube
Figure L.4
Scanner with AutoLoader rear connections
appendix L | Using the GeneChip® AutoLoader
737
INDICATOR LIGHTS AND ON/OFF BUTTON
The front panel has the following button and indicators (Figure L.5).
Blue
Autoloader
Indicator
Light
Blue
Scanner
Indicator
Light
Green light
I/O (on/off)
button
Yellow light
Figure L.5
The AutoLoader indicator lights
I/O (on/off) button in the center.
2. Blue indicator light on scanner body, running vertical at front
center. This light extends to the bottom of the AutoLoader and is
always on when the scanner is on.
1.
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Affymetrix® GeneChip® Operating Software User’s Guide
Blue indicator light on AutoLoader, running vertical at front
center. This light appears to be merely an extension of the scanner
light. However, when on, it indicates that the AutoLoader door is
closed and locked. It will turn off when the door is unlocked.
4. Green and yellow light both on indicate scanner boot up in
progress.
3.
5.
Yellow light
On = Idle, laser is warming up (laser not ready, green off)
B. Off = System ready, no errors (Green on)
C. Flashing = Error
6. Green light
A.
On = System is ready to scan (yellow off)
B. Flashing = Scan in progress
A.
Summary of Indicator Lights
The table below summarizes the light conditions and their meaning.
Table L.1
Indicator lights
Condition
Green
Light
Yellow
Light
Blue
Scanner
Indicator
Light
Blue
AutoLoader
Indicator Light
Meaning
Initial boot up
Off
Off
On
Off
Initial power up; embedded PC
takes control
Scanner boot
up
On
On
On
Off
Embedded PC takes control of
scanner boot up
Laser warm up
Off
On
On
Off
Software enabled and laser is
warming up
System ready
On
Off
On
Off
Scanner ready for use and
AutoLoader door is unlocked
waiting to receive a carousel
appendix L | Using the GeneChip® AutoLoader
739
Table L.1
Indicator lights
Condition
Green
Light
Yellow
Light
Blue
Scanner
Indicator
Light
Blue
AutoLoader
Indicator Light
Meaning
Error
Off
Flashing
On
Off
Fatal error, reboot scanner and
software, AutoLoader door is
unlocked to remove carousel if
necessary
Scanning
Flashing
Off
On
On
Scanning is in progress and
AutoLoader door locked
Scanning
Flashing
Off
On
Off
Scanning is in progress and
AutoLoader door is unlocked
Installing and Configuring the E-mail System
In the event of an AutoLoader error condition, you can enable the
software to send an e-mail containing error information using
Microsoft Exchange server or SMTP.
The user sets up the e-mail system just once.
See the following sections for information on installing and
configuring the E-mail system:
• E-mail System Installation (see below)
• E-mail Messages (see page 744)
E-MAIL SYSTEM INSTALLATION
The instrument installation software is on a separate CD. Use this CD
and the following procedure to install the instrument control software.
Launch Microsoft® Windows® 2000 Explorer.
2. Double-click setup.exe within the Instrument folder.
The Welcome window appears.
3. Click Next.
1.
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Affymetrix® GeneChip® Operating Software User’s Guide
Several consecutive Software License Agreement windows appear.
4. Click Yes in each window to accept the terms of the agreement.
5. The Choose Destination Location window appears.
6. Click Browse and select the Destination to install the instrument
driver (select the same location where you installed GCOS).
7.
Click Next.
The Select Components window appears (Figure L.6).
Figure L.6
The Select Components window, only the Affymetrix Scanner files box checked
8.
Remove the check from the Fluidics station and Sealevel card
files box. Select only the Affymetrix Scanner Files option.
Highlight the Affymetrix Scanner Files option and click
Change... to select the type of scanner. The following dialog box
opens and displays the choice of scanners, Affymetrix® GCS 3000
Scanner and GeneArray® 2500 Scanner (Figure L.7).
appendix L | Using the GeneChip® AutoLoader
741
Figure L.7
The Select Sub-components window, only the Affymetrix Scanner files box
checked
Select the Affymetrix® GCS 3000 Scanner and click Continue.
10. Click Next.
The Email Option window appears (Figure L.8).
9.
Using Microsoft® Exchange
If you are using Microsoft Outlook with Microsoft Exchange, you
must configure Outlook XP to work with the Exchange server.
Each user can set up an individual distribution list, and all users
share the same name for each of their own individual distribution
lists. Thus there can be two cases in sending e-mail:
- There is a single e-mail contact for everybody
- There is a common distribution list name, and every user must
set up a list with that name.
Configure it by the following steps.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure L.8
The Email Option window with Microsoft® Exchange Server checked
1.
Select the Microsoft Exchange Server. Enter an e-mail address or a
distribution list that has been set up in Outlook. To set up a
distribution list see the section below.
When an e-mail is sent during a normal run, you must be logged
into the workstation and have an account on the exchange server.
Setting up Outlook for a distribution list
Let us call the name of the distribution list AutoLoaderGroup.
Launch Microsoft Outlook.
2. On the File menu, point to New, and then click Distribution List.
3. In the Name box, type the name that is used in the Instrument
Install (e.g. AutoLoaderGroup).
4. Click Select Members.
1.
appendix L | Using the GeneChip® AutoLoader
743
In “Show names from the list,” choose the address book that
contains the e-mail addresses you want in your distribution list.
6. In the “Type name or select from list box,” type a name you want
to include, or select a name from the list below, and then click
Members. Do this for each person you want to add to the
distribution list, and then click OK.
If you want to add a longer description of the distribution list,
click the Notes tab, and then type the text.
5.
7.
You save the distribution list in your Contacts folder by the name
you give it.
All e-mail generated during an AutoLoader run will be sent to the
people in the distribution list
Each user, who plans to run the AutoLoader through his/her user
account, should create a distribution list.
Configuring SMTP
If you are using SMTP, configure it as follows.
Figure L.9
The e-mail contact configuration window with SMTP configured
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Affymetrix® GeneChip® Operating Software User’s Guide
Enter the IP address of the SMTP server and the port number at
which SMTP transactions occur.
2. Enter an e-mail address or comma separated list of e-mail addresses
to which the e-mail must be sent.
1.
No E-mail Options
Select this option to disable the e-mail system. Place a check in box
None.
E-MAIL MESSAGES
If the e-mail system is enabled, the instrument control software sends
an e-mail alert for conditions that may occur during an AutoLoader
run.
For a list of serious errors, see AutoLoader Error Messages, on
page 789.
In case of a fatal error:
1.
The software sends an e-mail to the specified set of e-mail addresses
or to the Outlook distribution list.
The software provides you with the ability to send an e-mail
without your intervention.
3. The software uses extended MAPI to send an e-mail.
4. Each e-mail message contains the following information:
2.
Date and Time
B. Scanner ID
C. All experiment information displayed in the status window.
Table L.2 lists the relevant e-mail messages.
A.
appendix L | Using the GeneChip® AutoLoader
745
Table L.2
E-mail Message Conditions. These will appear on the scan status field of the
status screen at the bottom of the GCOS GUI such as the Experiment Information
Window. (See Troubleshooting, on page 787 for recommended action).
Condition
Detected By
Action/Mitigation
Carousel Home
Error
Carousel Home not detected
after more than one carousel
rotation
Log error, stop run,
notify user via GUI and
e-mail
Grip Home Error
Grip Home not detected after
more than full actuator travel, a
mechanical error
Log error, stop run,
notify user via GUI and
e-mail
Feeder Fail
Cartridge not detected in
scanner or AutoLoader during
load or unload
Log error, stop run,
notify user via GUI and
e-mail
Load Request
Error, Cartridge
in Scanner
Cartridge already in scanner
when software directs
AutoLoader to load a cartridge
Log error, stop run,
notify user via GUI and
e-mail
Unload Error,
Cartridge in
AutoLoader
Cartridge detected already in
AutoLoader when software
directs AutoLoader to unload a
cartridge (Autoloader cannot
unload the cartridge.)
Log error, stop run,
notify user via GUI and
e-mail
Cooling Over
Temperature
Cooling set point not attained
within 1 hour of activation
Log error, disable
cooling, notify user via
GUI and e-mail,
continue AutoLoader
run
Cooling Under
Temperature
Cooling temperature < 5ºC
Log error, disable
cooling, notify user via
GUI and e-mail,
continue AutoLoader
run
Door Opened
Door was opened in the middle
of a scan causing current chip to
be rescanned
Log error and e-mail
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Affymetrix® GeneChip® Operating Software User’s Guide
Table L.2 (Continued)
E-mail Message Conditions. These will appear on the scan status field of the
status screen at the bottom of the GCOS GUI such as the Experiment Information
Window. (See Troubleshooting, on page 787 for recommended action).
Condition
Detected By
Action/Mitigation
Power failure/
restore
Power was lost/or restored to
the workstation and /or
AutoLoader
If a UPS is attached to
the workstation, an email will be sent
Network
disconnect
A network disconnect between
workstation and scanner was
detected
Log error and e-mail
user
End of Run
Scanner stops the AutoLoader
run upon encountering a chip
previously scanned or after
scanning 48 chips
Notify user via GUI and
e-mail that the run has
completed
Operating the Scanner-AutoLoader
This chapter describes how to use GCOS to control the Affymetrix®
GeneChip® Scanner and AutoLoader (Figure L.1).
appendix L | Using the GeneChip® AutoLoader
747
define experiment (*.exp)
Process probe array in fluidics station
Scan probe array
(save image to *.dat)
Compute cell intensity data
(save intensity data to *.cel)
Analyze *.cel
(save results to *.chp)
Generate report (*.rpt)
Figure L.10
Assay & analysis flow chart
Quick Reference Walkthrough
The table below illustrates the steps required to scan a set of probe
arrays.
748
Step
1. Enter and save the
experiment
information in the
Experiment
Information Window.
For more information, see The
Experiment Information
Window, on page 758.
2. Hybridize the probe
arrays.
For more information, see the
GeneChip® Expression
Analysis Technical Manual and
relevant package inserts.
Affymetrix® GeneChip® Operating Software User’s Guide
Description
appendix L | Using the GeneChip® AutoLoader
Step
3. Wash the probe
arrays.
For more information, see the
GeneChip® Fluidics Station
450/250 User’s Guide and
relevant package inserts.
4. Apply Tough-Spots®
For more information, see
Using Tough-Spots® to Prevent
Leaks, on page 763.
Description
749
750
Step
5. Load probe array
cartridges into
carousel.
For more information, see
Loading Cartridges into the
Carousel, on page 767.
6. Load carousel into the
AutoLoader. Set
properly by turning it
to set flush with
housing. Close the
door.
For more information, see
Loading the Carousel into the
AutoLoader, on page 769.
Affymetrix® GeneChip® Operating Software User’s Guide
Description
appendix L | Using the GeneChip® AutoLoader
Step
7.
751
Description
Start the AutoLoader
run.
For more information, see
Scanning a Probe Array in
Automode, on page 771.
• If you want to scan the probe arrays without waiting for them to have
warmed up, check box.
• If you want to rescan currently loaded probe arrays that had been scanned in
a previous run, check Allow rescans box. The .dat file from the previous run
will not be overwritten.
The AutoLoader Run
This section shows you how to scan multiple GeneChip® probe arrays
using the new Affymetrix® GeneChip® Scanner 3000 equipped with
the AutoLoader.
Figure L.11
Affymetrix® GeneChip® probe array cartridge: note the location of the flange.
The AutoLoader will accept the cartridge in only one orientation.
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Affymetrix® GeneChip® Operating Software User’s Guide
The Autoloader operation is described in more detail in the following
sections:
• Quick Reference Guide to Using the AutoLoader (see below)
• The Experiment Information Window (see page 758)
• Turning on the Scanner-AutoLoader (see page 762)
• Using Tough-Spots® to Prevent Leaks (see page 763)
• Using the Barcode Reader (see page 765)
• Loading Cartridges into the Carousel (see page 767)
• Loading the Carousel into the AutoLoader (see page 769)
• Scanning a Probe Array in Automode (see page 771)
• Scanning a Probe Array in Manual Mode (see page 777)
• Stopping an AutoLoader Run (see page 782)
• Shutting Down the Scanner (see page 783)
• Using GCOS without a Scanner. (see page 783)
• Using GCOS with the AutoLoader Disabled. (see page 784)
• Turning on the Laser at GCOS Launch (see page 786)
QUICK REFERENCE GUIDE TO USING THE AUTOLOADER
The following table can help you find specific procedures based on the
type of task you are looking for.
If you want to:
Then do this:
Use the AutoLoader in
automode
1. Click Tools → Defaults.
2. Clear the check box Enable Manual Mode.
3. Click OK (Figure L.21).
appendix L | Using the GeneChip® AutoLoader
If you want to:
Then do this:
Use the AutoLoader in
manual mode
1. Click Tools → Defaults.
753
2. Check Enable Manual Mode.
3. Click OK (Figure L.24).
Turn on the laser
immediately when you
launch GCOS
1. Click Tools → Defaults.
2. Check Turn on Laser at startup.
3. Click OK (Figure L.30).
Add an experiment
1. Open the GCOS software, and click Experiments.
Information window.
to open the Experiment
2. Enter and save the experiment information in the Experiment Information Window.
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Affymetrix® GeneChip® Operating Software User’s Guide
If you want to:
Then do this:
Add a barcode
1. Open the GCOS software to the Experiment Information window.
• Note: A new experiment
must be opened for each
barcode.
2. Place cursor in the barcode field.
3. Hold a GeneChip probe array cartridge in front of the barcode reader and squeeze
the trigger for up to four seconds until you hear a beep.
The reader reads and sends the barcode to the GCOS Experiment Information
window, Barcode field. The software automatically fills other fields.
4. After the software adds the barcode, save the experiment.
5. Repeat steps 1 to 4 until you have read all of the probe array cartridges.
appendix L | Using the GeneChip® AutoLoader
If you want to:
Then do this:
Start a scanning run
1. Load the carousel and place the carousel into the AutoLoader.
2. Click the Start button
.
• If the arrays are at room temperature, or you want to scan the probe arrays
without waiting for them to warm up, check the appropriate box.
• If you want to allow the probe arrays to be
rescanned, check the appropriate box.
(The rescan function is handy if you want to
rescan a currently loaded probe array that
had been scanned in a previous run.)
3. Click OK. The AutoLoader homes and
performs an inventory of the probe arrays
and the scanning run begins.
755
756
If you want to:
Affymetrix® GeneChip® Operating Software User’s Guide
Then do this:
Add a probe array during a
scan
1. Click the Add button
or select Run → Add Chips.
• If you want to unlock the door and immediately begin adding cartridges, click the
Add Now button. The blue indicator light on the front of the AutoLoader will go
out signifying that the door is unlocked and you can load more cartridges.
The cartridge being scanned, if any, will be rescanned, and the previously created
.dat file WILL BE OVERWRITTEN.
• If you want to wait for the scan to complete before adding a probe array, click
the Add after Scan button. The current scan will continue until completion, then
the door will unlock and you can load more cartridges. The Autoloader blue
indicator light will go out to signify that the door is unlocked.
• In both cases, after you have added your cartridges and closed the door, the
following window will appear. Click OK.
2. Click the Resume
button or Run → Resume. The door then locks and the
blue indicator light turns on.
Use GCOS without a
scanner
1. Click Tools → Defaults.
2. Clear the check box Scanner Installed.
3. Click OK (Figure L.28).
Disable AutoLoader and
use the scanner only
1. Click Tools → Defaults.
2. Check Disable AutoLoader.
3. Click OK (Figure L.29).
appendix L | Using the GeneChip® AutoLoader
If you want to:
Stop a scan
757
Then do this:
1. Click the Stop button
.
2. When the following window
appears, click OK.
Caution: If you stop the scanner
while a probe array is in the
process of scanning, you will lose
all scan information from that probe array. If you rescan the array, it may be affected
due to uneven photo-bleaching. This could potentially make the data from the array
difficult to compare to other array data.
Terminating a scan run
The AutoLoader run will terminate under certain normal
circumstances. Table L.2 outlines under what conditions a scan run will
or will not terminate.
Table L.3
Summary of scan run termination conditions
The scan run will terminate if:
The scan run will not terminate if:
You press the Stop button. Caution: If you
stop the scanner while a probe array is in
the process, you will lose all scan
information from that probe array. If you
rescan the array, it may be affected due to
uneven photo-bleaching. This could
potentially make the data from the array
difficult to compare to other array data.
You check Allow Rescans box. When the AutoLoader
encounters a probe array that was previously scanned in an
earlier run, it will rescan that probe array and will create
additional .dat files (.dat1, .dat2, etc.).
The AutoLoader detects a probe array with
the same barcode in the current run, i.e., in
the currently loaded carousel. The probe
array will not be rescanned.
You clear the Allow Rescans box. When the AutoLoader
encounters a probe array that was previously scanned in an
earlier run, it will log the probe array but will not rescan it. It
will continue the run.
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Affymetrix® GeneChip® Operating Software User’s Guide
Table L.3 (Continued)
Summary of scan run termination conditions
The scan run will terminate if:
The scan run will not terminate if:
The AutoLoader detects 48 scanned
cartridges in the same run.
You click the Add Now button. The AutoLoader door will
unlock to accept new probe array cartridges. The scan in
progress will complete. When you close the door and
continue, the AutoLoader will home, take inventory and move
to the same probe array that was in the process of being
scanned when the door was opened. It will discard the earlier
.dat file and rescan that probe array.
Note: this has nothing to do with the Allow Rescans check
box.
You click the Add After Scan button. The AutoLoader door
will wait until the scan in progress is complete then unlock
the door. When you close the door and continue, the
AutoLoader will home, take inventory and move to the next
probe array from that which was in the process of being
scanned when the door was opened.
THE EXPERIMENT INFORMATION WINDOW
The Experiment Information window (EIW) provides you with the
means for generating and saving a database of your experimental data
(Figure L.15).
Before you can advance to the next experiment, you must first save
the current experiment.
Certain information has to be entered before the experiment can be
saved. Table L.4 lists the available fields and their definitions and
whether or not they are required in order to save the experimental
data.
For more information, see Registering a Sample & Defining an Experiment,
on page 80.
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759
Table L.4
Definitions of the experiment data fields in the Experiment Information Window
Field
Definition
Required for
save
Sample Template
Dropdown box for templates
associated with samples
No
Sample Name
The name of the sample.
Yes
Sample Type
The type of sample. This is an
attribute of the sample that
describes its type. Example: blood,
cell line, tissue, etc.
Yes
Sample Project
The name of the project associated
with the sample.
Yes
Sample owner
Read-only field showing the owner
of the sample in the database.
Yes
Experiment
Template
Dropdown box for experiment
templates
No
Experiment Name
The name of the experiment.
Yes
Probe Array Type
This is the probe array type
associated with the experiment,
and automatically filled in when
you enter the barcode.
Yes
Barcode
User entered barcode
Yes (No if
AutoLoader is in
manual mode)
Expiration Date
Array Expiration date embedded in
Affymetrix barcode, and
automatically filled in when you
enter the barcode.
No
Probe array Lot
number
Array lot number embedded in
Affymetrix barcode, and
automatically filled in when you
enter the barcode.
No
Experiment owner
Read-only field showing
experiment owner
Yes
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Affymetrix® GeneChip® Operating Software User’s Guide
Table L.4 (Continued)
Definitions of the experiment data fields in the Experiment Information Window
Field
Definition
Required for
save
User-set
Drop down list of user-sets in the
database used for storing analysis
parameters
No
Publish Database
Drop down list of names of the
publish databases. Used when
selecting automation
No
Publish Intensities
Checkbox to be selected if
publishing intensities to the
database after completing the
analysis
No
Scan Status Window
GCOS software provides you with the status of all scans, the status of
the AutoLoader door and status of the current scan. This window is
located at the bottom of user interface (Figure L.12). Below
(Table L.5) describes the status fields.
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Status
window
Figure L.12
The scan status window
Table L.5
The GCOS Status Fields and Descriptions
Status Field
Description
Position
Position occupied by a given cartridge in the
AutoLoader carousel
Experiment Name
The experiment name associated with the scan
associated with a given cartridge position
Probe Array Type
The probe array type for the scan associated with
a given cartridge position
Barcode ID
The unique identifier in the barcode for the scan
associated with a given cartridge position
User
Name of the user (experiment owner) for the scan
associated with a given cartridge position
Time & Date
The date and time when scan started and
completed
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Table L.5 (Continued)
The GCOS Status Fields and Descriptions
Status Field
Description
Scan Status
The status of the scan. (Autofocus, scanning). This
field displays all scanner status strings associated
with the scan and retrieved from the scanner.
The message strings that may appear in this field
are listed below.
Note: Not all of these messages will appear in
each AutoLoader run.
Status Field Strings
Autofocus
Scan Status - % of lines scanned
Scan Complete status
Grid alignment errors
Autofocus Errors
The experiment XXX has already been
scanned
Chip load failures
Invalid barcode errors
Experiment does not exist errors
AutoLoader door open errors
AutoLoader Door (viewed
in status bar)
The status of the AutoLoader door
Number of Cartridges
(viewed in status bar)
Number of cartridges in the AutoLoader carousel
as determined by inventory
History
(viewed as a log)
A running history of the last 99 arrays scanned and
the information on the current array (if any) being
scanned
TURNING ON THE SCANNER-AUTOLOADER
Press the on/off (I/O) switch on the front panel. The scanner’s onboard
computer will boot up. The bootup process takes a few of minutes.
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During this time both the yellow and green light will be on. The
scanner enters the laser warm-up state. During this warm-up time, the
green light will turn off and the yellow light will remain on. You must
wait 10 minutes for the laser to stabilize.
USING TOUGH-SPOTS® TO PREVENT LEAKS
Tough-Spots® are chemically inert polyvinyl labels that adhere to all
plastics. Affymetrix recommends using 3/8-inch circle diameter
Tough-Spots to prevent leakage from the cartridge septa.
Before loading the probe array cartridge, follow this procedure to
prevent the leaking of fluids from the cartridge during scanning.
Even if you have already applied Tough-Spots to the cartridge prior to
hybridization or after washing, you must remove the old Tough-Spots
and apply new ones before you load them into the AutoLoader.
Affymetrix recommends the use of Tough-Spots® obtained from
Affymetrix P/N 64-0158
or from
USA Scientific, Inc. P.O. Box 3565 Ocala, FL 34478 (800)LABTIPS P/N 9185-0000
To reduce the risk of leakage, do not use excessively large pipette
tips to pierce the septa.
1.
On the back of the probe array cartridge, clean excess fluid from
around septa (Figure L.13).
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure L.13
The GeneChip® probe array cartridge
2.
Carefully apply one Tough-Spot over each of the two septa. Press
to ensure that the spots remain flat. If a Tough-Spot does not apply
smoothly; that is, if you observe bumps, bubbles, tears or curled
edges, do not attempt to smooth them out. Remove the spot and
apply a new one (Figure L.14).
Tough-SpotsTM
Figure L.14
Applying Tough-Spots® to cartridge septa
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USING THE BARCODE READER
If you have not already done this during the initial experiment setup,
you must now add a new barcode for each experiment.
1.
Open the GCOS software to the Experiment Information window
and place the cursor in the barcode reference field of the GCOS
Experiment Information window (Figure L.15).
You should open a new experiment and place the cursor into the
barcode field before triggering the reader. Otherwise, the barcode
will be misinterpreted as some other kind of input. A new
experiment has to be opened for each barcode, and certain other
information has to be entered before the experiment can be saved.
Figure L.15
Experiment Information Window with cursor in the barcode field
766
2.
Affymetrix® GeneChip® Operating Software User’s Guide
Hold a GeneChip probe array cartridge in front of the barcode
reader and squeeze the trigger for up to four seconds until you hear
a beep (Figure L.16).
Figure L.16
Reading the cartridge barcode
3.
The reader reads and sends the barcode to the GCOS Experiment
Information window, Barcode field (Figure L.17).
The software also automatically fills in the “Probe Array Type,”
“Probe Array Lot,” and “Expiration Date” fields. These are readonly fields.
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767
Figure L.17
After the software adds the barcode, save the experiment.
5. Repeat steps 1 to 4 until all of the probe array cartridges have been
read.
4.
LOADING CARTRIDGES INTO THE CAROUSEL
1.
Load your cartridges into the carousel (up to 48). Note that only
one orientation is possible (Figure L.18).
Cartridges should be loaded into the carousel starting at position
#1. Additional cartridges need not be contiguous. A run will stop
after 48 cartridges OR when the same barcode is read within the
same run.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure L.18
Loading the cartridge into the chip carousel, note that each slot is numbered., 1
through 48, and each cartridge can fit in only one orientation
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LOADING THE CAROUSEL INTO THE AUTOLOADER
1.
Load the carousel into the AutoLoader by inserting the carousel
into the AutoLoader and turning the carousel until the alignment
pin seats into the alignment hole (Figure L.19)
Alignment
Hole
Carousel
Mounting
Key Flat
Alignment
Key in the
Autoloader
Alignment
Pin
Figure L.19
Loading the cartridge carousel into the AutoLoader
770
2.
Affymetrix® GeneChip® Operating Software User’s Guide
Turn the carousel clockwise until the carousel mounting key flat
seats gently into the AutoLoader alignment key. You may have to
turn the carousel several times before it will seat into the
alignment pin and alignment key. When seated properly, the
carousel will be flush with the AutoLoader housing. Close the
AutoLoader door (Figure L.20).
Figure L.20
Inserting and turning the carousel; the carousel should be seated and flush with
housing.
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771
The seating of the key flat is confirmed by a gentle falling of the
carousel into the key.
SCANNING A PROBE ARRAY IN AUTOMODE
If all probe arrays have valid, associated barcodes, you can run the
AutoLoader in automode.
If there exists an identical barcode within the database from an
earlier AutoLoader run, and you want to rescan the current probe
array with that same barcode, check the Allow Rescans box
(Figure L.22). This will create additional .dat files. The original .dat
file WILL NOT BE OVERWRITTEN.
However, if the AutoLoader encounters the same barcode within
the same run, the run will terminate.
1.
Set the default settings.
Click Tools → Defaults (Figure L.21).
B. Clear the check box of Enable Manual Mode.
C. Click OK.
A.
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Figure L.21
Defaults window showing “Enable Manual Mode” with the check box cleared
2.
Click the Start button
in the Instrument Control shortcut bar
or the main toolbar; or
Select Run → Start Scanner from the menu bar.
The Start window appears (Figure L.22).
Figure L.22
The Start Scanner window in automode
If you have not already loaded your probe array cartridges, do so
now.
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773
If you want to skip the ten minute warm-up period before
scanning the first probe array, keep the default check in the Arrays
at room temperature box.
3.
Click OK in the GeneChip Scanner dialog box to start the run.
- The AutoLoader blue indicator light will light up signifying
that the AutoLoader door is now locked.
- The carousel automatically homes itself and performs
inventory to determine the number and position of cartridges
present.
- The scanning run begins. During the scan, the green light will
flash, and the yellow light will be off.
- The AutoLoader completes the autofocus operation before
scanning each of the probe arrays. This takes approximately
two to three minutes. The scanner cannot be stopped during
this period.
- The run will stop automatically when the last cartridge is
scanned.
- At the completion of each scan, the GCOS software will
attempt grid alignment. If it is successful, the scan data will be
automatically advanced to the Grid Alignment processing
state.
- If the View Scan In Progress feature is enabled (select View →
Scan in Progress from the menu bar), the Image window
automatically opens in the main display area when a scan
starts. It displays the fluorescence intensity of the probe array
at approximately 200 lines at a time as the scan progresses.
- To enable (or disable) this option, select View from the menu
bar and place (or remove) a check mark next to Scan in
Progress.
After the scan is completed, GCOS:
A.
saves the image data to an image data file (*.dat) (displayed in
the main display area)
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aligns a grid on the *.dat to identify the probe cells
C. automatically computes probe cell intensities and saves the data
to the cell intensity file (*.cel)
D. ejects the probe array.
The AutoLoader will skip probe array cartridges if the AutoLoader
encounters:
B.
A.
cartridges with unreadable or invalid barcodes or without
barcodes
cartridges with barcodes that are not associated with an
experiment
C. cartridges that have been previously scanned if the Allow
Rescans checkbox is cleared (Figure L.22).
B.
AUTOROTATION
The AutoLoader is equipped with a heater to warm up the
cartridges prior to scanning in order to reduce condensation and
fogging of the probe array cartridge window.
The autorotation routine is used for temperature stability but only
after the AutoLoader run is complete or during a power failure as
described below.
Autorotation occurs during a power failure only if the uninterrupted
power supply (UPS) is included as an accessory. The UPS provides
power to the scanner/AutoLoader during a power failure. If the
power fails during the scan of an array, that scan is completed and
then the system turns off the heater and enters the autorotation
mode to conserve power and cool the chips in the carousel. The
system will also attempt to send an e-mail to notify the user of the
power failure.
During an AutoLoader run, the carousel is rotating as the chips are
processed to introduce the next chip to the scanner, so autorotation
is not needed. After the AutoLoader run is complete the heater is
turned off and the carousel is rotated to get even cooling of the
chips.
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775
Adding Cartridges during a run
The software provides you with a button that will allow you to unlock
the AutoLoader door and add additional probe array cartridges while
in the middle of an AutoLoader run. You have two choices: to add
cartridges immediately even while a scan is in progress (in which case
the .dat file is discarded and replaced with a newly collected one after
the AutoLoader run is resumed), or, as a second choice, to add
cartridges after a scan has completed (in which case the .dat file is
saved).
The Add Chips button is enabled only after the AutoLoader has
started a run in automatic mode.
Click the Add Chips button
, or select Run → Add Chips from
the menu bar.
The software displays a dialog box with three buttons (1) Add
Now (2) Add after scan is complete (3) Cancel (Figure L.23).
Figure L.23
The Add Chips selection buttons
1.
If you click the Add Now button:
A.
The blue AutoLoader indicator light will turn off signifying
that the AutoLoader door is now unlocked. Open the door and
add probe array cartridges.
If a scan is in progress, the software will continue to record the
scan. However, to avoid the possibility of generating a corrupt
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.dat file, it will discard that scan that was in progress when the
door was opened.
The Resume button
procedure.
is available only for the Add Chips
B.
After you have added your cartridges, close the door and the
following window appears.
C.
Click OK and then click the Resume
button or select Run
→ Resume.
The blue AutoLoader indicator light turns on signifying that
the door is locked. The software homes the carousel and
inventories the number of present probe arrays. The carousel
then moves to that last previously scanned probe array
(when the door was opened) and continues the scanning
run by rescanning that probe array cartridge.
The cartridge is rescanned and a new.dat file overwrites the
previous .dat file.
Do not load a cartridge into the same carousel position that was
occupied by the cartridge that had just been scanned, i.e., do not
replace cartridges.
2.
If you click the Add after scan is complete button,
A.
The AutoLoader will wait until the current probe array
cartridge has undergone the autofocus and scan procedures
before unlocking the door to allow you to add probe array
cartridges.
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777
The blue AutoLoader indicator light will turn off signifying
that the AutoLoader door is now unlocked.
C. Open the door and add probe array cartridges.
D. After you have added your cartridges, close the door and the
following window appears.
B.
The GCOS status bar will also display a “waiting to start”
status.
Click OK and then click the Resume
button or select Run
→ Resume.
The blue AutoLoader indicator light turns on signifying that
the door is locked. The software homes the carousel and takes
inventory of the probe array cartridges present. The carousel
then proceeds to the next cartridge position following the
previously scanned probe array. The AutoLoader continues
the run from that cartridge position.
3. If you click the Cancel button, the AutoLoader will continue the
AutoLoader run.
E.
SCANNING A PROBE ARRAY IN MANUAL MODE
In the AutoLoader Automode, each probe array cartridge requires a
valid barcode in order to be scanned. The manual mode feature allows
you to scan one probe array at a time without the requirement of a
barcode. This is useful if you must scan probe arrays that have invalid
or absent barcodes.
1.
Set the default settings.
A.
Click Tools → Defaults (Figure L.24).
Check Enable Manual Mode.
C. Click OK.
B.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure L.24
Enable Manual Mode checked
2.
Click the Start button
in the Instrument Control shortcut
bar or the main toolbar; or
Select Run → Start AutoLoader from the menu bar
(Figure L.25).
appendix L | Using the GeneChip® AutoLoader
779
Figure L.25
The Scanner control window
The scanner Start window appears. At this point, you can choose
from a number of options:
You can click Start without selecting an experiment. If your
cartridge has a valid barcode, the software will get the barcode
from the cartridge in the AutoLoader and select the correct
experiment.
2. If your cartridge has a valid barcode, you can scan the barcode on
the probe array cartridge in to the barcode field. The software will
retrieve the experiment associated with the array.
3. If your cartridge does not have a valid barcode, you can manually
select an experiment as described below.
1.
A.
The Experiment Name drop-down list displays the
experiments (*.exp) in the current directory that have not been
scanned (no *.dat file containing scan data exists for the
experiments).
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Affymetrix® GeneChip® Operating Software User’s Guide
B.
To include scanned experiments in the Experiment Name
drop-down list, choose the Include Scanned Experiments
option.
If filters have been applied in GCOS Server mode, the drop-down
list may not include all experiments. Click Filter to open the Filters
dialog box and view or specify filters.
Select the experiment name of the probe array to be scanned
from the Experiment Name drop-down list.
- The Probe Array Type field automatically displays the probe
array type that was entered during experiment setup. GCOS
sets the Number of Scans per probe array type (one for the
GeneChip® Scanner 3000).
- You may change the number of scans in the Scanner dialog
box (Figure L.25). Multiple scans are statistically averaged to
create a single image data file (*.dat).
C.
Increasing the number of scans increases the scan time as well as
the amount of fluorophore bleaching and may result in lower
fluorescence intensities.
Click Start.
The Scanner dialog box appears (Figure L.26).
D.
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781
Figure L.26
The start scanner window in manual mode
- You can check Array at room temperature if you want to
skip the ten-minute warm-up period before scanning the
probe array. The default has the box already checked.
You can eject or load a cartridge by clicking on the Load/Eject
button at any time except during the time the scanner is engaged in
the autofocus operation or the scanning run.
4.
Load the probe array cartridge into slot number 1.
The cartridge slot at position number 1 is the only slot available in
Manual Mode.
5.
Click OK in the Start Scanner box (Figure L.26) to start the
autofocus routine. This takes approximately two to three minutes.
The scanner cannot be stopped during this period.
During the scan, the green light will flash, and the yellow light
will be off.
If the View Scan In Progress feature is enabled (select View →
Scan in Progress from the menu bar), the Image window
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Affymetrix® GeneChip® Operating Software User’s Guide
automatically opens in the main display area when a scan starts. It
displays the fluorescence intensity of the probe array at
approximately 200 lines at a time as the scan progresses.
To enable (or disable) this option, select View from the menu bar
and place (or remove) a check in the box next to Scan in Progress.
After the scan is completed, GCOS:
saves the image data to an image data file (*.dat) (displayed in
the main display area)
B. aligns a grid on the *.dat to identify the probe cells
C. automatically computes probe cell intensities and saves the data
to the cell intensity file (*.cel)
A.
D.
ejects the probe array.
Ejecting a probe array cartridge
The probe array cartridge will automatically eject after a run; however,
if you must eject a cartridge, click the Load/Eject button
(Figure L.25). This command is only available in manual mode.
This completes the manual mode section.
STOPPING AN AUTOLOADER RUN
The Stop button is only available after you have clicked the Start
button. Click this button if you want to abort a scan or run in progress.
If you stop the scanner while a probe array is in the process, you will
lose all scan information from that probe array. If you rescan the
array, it may be affected due to uneven photo-bleaching. This could
potentially make the data from the array difficult to compare to
other array data.
1.
Click the STOP toolbar button
from the menu bar.
or select Run → Stop Scanner
appendix L | Using the GeneChip® AutoLoader
2.
783
At the prompt, click Yes to stop the scanner or No to elect not to
stop the AutoLoader run (Figure L.27).
Figure L.27
Stop AutoLoader prompt
3.
A window will display the message “The scanner will not stop
until autofocus has finished.” Click OK. After you stop a scan, the
scanner will automatically eject the cartridge.
SHUTTING DOWN THE SCANNER
Close the GCOS software. This is the best way to shut off the laser.
2. Press the I/O button on the front panel to turn off the instrument.
1.
USING GCOS WITHOUT A SCANNER.
In the event that you would like to use GCOS and do not have or do
not want to attach a scanner, you should clear the check box of the
Scanner Installed option in the Defaults window. This will prevent the
software from continually attempting to make contact with the
scanner.
Click Tools → Defaults.
2. Clear the check box of Scanner Installed (Figure L.28).
3. Click OK.
1.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure L.28
Scanner Installed with the check box cleared
USING GCOS WITH THE AUTOLOADER DISABLED.
If you have a working scanner but the AutoLoader is not operating,
you can still use the scanner, but you must check the Disable
AutoLoader option in the Defaults window. This will disable the
AutoLoader and enable you to use the scanner alone as you would in
manual mode.
Click Tools → Defaults.
2. Check Disable AutoLoader.
3. Click OK (Figure L.29).
1.
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785
Figure L.29
Disable AutoLoader checked
A window will appear
asking that you reboot the
scanner.
4. Press the scanner front panel
I/O button once to turn off
the scanner (Figure L.5). Wait a few moments, the press the I/O
button to turn on the scanner.
Open the AutoLoader door.
6. Manually load a probe array cartridge into the slot.
7. Close the AutoLoader door.
8. Scan the probe array in the same manner as the AutoLoader in
manual mode. See Scanning a Probe Array in Manual Mode, on
page 777.
5.
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Affymetrix® GeneChip® Operating Software User’s Guide
After scanning the probe array, you must manually remove the
probe array cartridge from the AutoLoader. See Steps 7 though 13
in Manually Removing a Lodged Probe Array Cartridge, on page 790.
TURNING ON THE LASER AT GCOS LAUNCH
You have two options as to how to control the actuation of the laser.
You can have the GCOS software turn on the laser at the launch of the
GCOS software. This allows you to begin the ten-minute warmup
period immediately. Or you can wait until you are about to run a series
of probe array cartridges to turn on the laser. You still wait ten
minutes for the laser to warm up.
1.
Click Tools → Defaults (Figure L.30).
If you want to turn on the laser immediately upon launching
the GCOS software, check Turn on Laser at startup.
B. If you want to wait until you are ready to run a scanning
procedure, before turning on the laser, clear the check box for
Turn on Laser at startup.
2. Click OK.
A.
appendix L | Using the GeneChip® AutoLoader
787
Figure L.30
Turn on Laser at startup checked
Cleaning and Maintenance
The AutoLoader requires little in the way of customer maintenance.
The instrument must be kept clean and free of dust. Dust buildup can
degrade performance. Wipe the exterior surfaces clean using a mild
dish detergent solution in water. Do not use ammonia based cleaners
or organic solvents, such as alcohol or acetone, to clean the system
because they may damage the exterior surfaces.
Clean the carousel by hand using warm water and, if necessary, mild
detergent.
Troubleshooting
Troubleshooting tips are given in the table below and in the following
sections:
• AutoLoader Error Messages (see page 789)
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• Manually Removing a Lodged Probe Array Cartridge (see page 790)
Problem
Possible Cause
No image when scanning • Power off or cable loose
Corrective Action
Check all connections and power.
• Loss of laser power
Contact technical support.
• Image display disabled
Enable image display
Intermittent problems
scanning
• Loose cable
Check all rear connections.
Scanner fails with probe
array inside
• Power failure
Manually extract probe array. Check all
connections to scanner. Turn scanner on,
restart software.
Carousel does not
automatically home
• Check for stuck cartridge
• Carousel not seated on D
ring
• Alignment Pin not engaged in
Carousel
• Door is open or ajar
• Door is open when blue LED
is off.
Carousel does not rotate
• Door is open or ajar
• System is warming up, chip
in heater
• Carousel not seated on D
ring
• Alignment Pin not engaged in
Carousel
• Laser in Scanner is warming
up. GCOS has Start grayed
out in this case
Carousel misses next chip • Cartridge UP sensor not
working, call technical
support.
Stuck cartridge
AutoLoader freezes up
See Manually Removing a Lodged Probe
Array Cartridge, on page 790
• Door is open or ajar
appendix L | Using the GeneChip® AutoLoader
Problem
AutoLoader overheats
Possible Cause
789
Corrective Action
• Heater Failure
Call technical support.
• TE failure
Call technical support.
• TE hot fans vent blocked
Autofocus routine fails to
conclude
• Try to rescan chip.
• Check for salt on chrome border. If still error,
call technical support.
The cartridge does not
descend into scanner.
• Carousel not seated correctly
• Door is open or ajar
• Heater is waiting until chip is
at temperature.
AUTOLOADER ERROR MESSAGES
The following error messages indicate a serious malfunction of the
scanner with AutoLoader. Your probe arrays, or the data generated
from them, may be at risk. You should shut down the AutoLoader and
remove the carousel. Do not continue to use the AutoLoader in
Automode. Call Affymetrix Technical Support.
However, if the AutoLoader appears to be operating normally,
you can continue to use the AutoLoader in Manual Mode. See
Scanning a Probe Array in Manual Mode, on page 777.
HEATER_LOW
“Warning: The warming chamber temperature is low.
Refer to the troubleshooting guide.”
COLD_CHAMBER_LOW
“Warning: The cold chamber temperature is low. Refer
to the troubleshooting guide.”
COOL_HOTSIDE_HIGH
“Warning: The cooler hot-side temperature is high.
Refer to the troubleshooting guide.”
Note: Before calling technical support, check
around the ventilation vents to ensure that
nothing is blocking them.
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Affymetrix® GeneChip® Operating Software User’s Guide
COLD_CHAMBER_HIGH
“Warning: The cold chamber temperature is high.
Refer to the troubleshooting guide.”
Note: Before calling technical support, check the
AutoLoader door to ensure that it is not open.
HEATER_HIGH
“Warning: The warming chamber temperature is high.
Refer to the troubleshooting guide.”
MANUALLY REMOVING A LODGED PROBE ARRAY CARTRIDGE
In the event that a probe array becomes lodged in the chip transport
mechanism, follow the procedure outlined below.
1. Turn the AutoLoader off and remove the power cord from the back of the unit.
2. Open the AutoLoader door on top of the unit.
3. Remove the carousel from the system. (Keep cartridges in carousel at proper temperature while
recovering the cartridge still in the scanner).
appendix L | Using the GeneChip® AutoLoader
791
4. Remove the hole
plug, which is just in
front of the
cartridge slot in the
base piece of
insulation. In the
photo to the left,
the screwdriver is
inserted into this
hole.
5. Using a standard, flat (-) screwdriver, (13-0257) gently slide it down through the hole making
sure not to damage the shaft and spring that are protruding into the hole. When the
screwdriver stops, it should be in contact with the scanner Y stage screw. Slowly turn the
screwdriver until you feel it engaging the slot on the screw of the scanner Y stage.
6. Slowly turn the screw clockwise until it hits a hard stop and cannot turn further. (Do not try to
turn it further or use excessive force because it will break the Y stage in the scanner). The Y
stage has now ascended to its maximum position.
792
7.
Using your fingers,
slowly slide the slot
pin, which is
sticking through the
slot in the base
piece of insulation,
to the right until it
stops. You should
see the little pinch
rollers near the
cartridge slot close
a little as you do
this.
Affymetrix® GeneChip® Operating Software User’s Guide
Pinch
Rollers
Slot
Pin
appendix L | Using the GeneChip® AutoLoader
8. Insert a 3/16” hex
driver (13-0255) into
the hole that is
located on the front
of the AutoLoader
housing on the left.
You should feel it
engage a coupling.
9. Turn the hex driver
counter clock wise
until you see the
cartridge appear
through its opening.
(The cartridge
should stay up if
you stop turning the
hex driver). If you
don't see the
cartridge after
turning the hex
driver ten seconds
go to step 11.
10. Grab and hold the cartridge with your fingers. Using your other hand slowly slide the slot pin
(Step 7) back to the left. This should open up the pinch rollers. Pull the cartridge out.
11. If you do not see the cartridge after turning the hex driver for 10 seconds, stop.
793
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Affymetrix® GeneChip® Operating Software User’s Guide
12. Using tool (13-0256)with the hook down and toward the back, slide it vertically down against
the front of the cartridge opening, about 1.5 inches. (There is a small groove made for this tool
in the middle of the front cartridge guide).
13. Pull the top finger grip of the tool toward the front of the unit, and then pull it up while still
putting pressure towards the front. The cartridge should come up with the tool. When you see
it, grab the cartridge and pull it out of the unit.
14. If you cannot get the cartridge out after doing this procedure, call for Affymetrix technical
support.
15. Put the hole plug back into the hole in the base piece of insulation.
16. Plug the scanner back in and turn it on.
17. Load the carousel after the scanner boots up.
18. If cartridges continue to become lodged in the AutoLoader, you should call technical support.
GeneChip® Scanner 3000 - AutoLoader Specifications
Item
Weight
Dimensions
Parameter
Value
Shipping
approx 115 pounds
(52.2 Kg)
Free-standing
approx 100 pounds
(45.4 Kg)
Width
~13.25 in.
Depth
~21.25 in.
Height
~32 in.
Power
See Scanner 3000
Specifications, on
page 576.
Working Environment
Temperature
59°F-85°F (15°C-30°C)
appendix L | Using the GeneChip® AutoLoader
Item
Parameter
795
Value
Humidity
10-90% Non-condensing
Clearance
2 in. (5 cm) on side, back
12.5 in. on top
Pollution Degree
2
Installation Category
II
Altitude
<2000m
Electrical Supply
See Scanner 3000
Specifications, on
page 576.
Main Supply Voltage
Fluctuations
See Scanner 3000
Specifications, on
page 576.
CE Mark Declaration of Conformity
We, Affymetrix, Inc.
4G Crosby Drive,
Bedford, Massachusetts
Declare under sole responsibility that the Affymetrix® GeneChip® Scanner 3000-AutoLoader conforms
with the relevant provisions of the following standards or other normative documents:
EU EMC Directive 89/336/EEC:
EN 61326:1998
Equipment for Measurement, Control and Laboratory
Use, EMC Requirements
EN 55011:1998
Industrial, scientific and medical (ISM) radio-frequency
equipment - Radio disturbance characteristics - Limits
and methods of measurement
EN 61000-3-2:2001
Limits for harmonic current emissions (equipment
input current up to and including 16 A per phase)
EN 61000-3-3:1995
Limitation of voltage changes, voltage fluctuations
and flicker in public low-voltage supply systems, for
equipment with rated current less than or equal to 16
A per phase and not subject to conditional connection
EN 61000-4-2:1995
Electrostatic discharge immunity.
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Affymetrix® GeneChip® Operating Software User’s Guide
EN 61000-4-3:1995
Radiated, radio frequency, electromagnetic field
immunity.
EN 61000-4-4:1988
Electrical fast transient/burst immunity.
EN 61000-4-5:1995
Surge immunity.
EN 61000-4-6:1996
Immunity to conducted disturbances induced by radio
frequency fields.
EN 61000-4-11:1994
Voltage dips, short interruptions, and voltage
variations immunity.
EU Low Voltage Directive 73/23/EEC
EN 61010-1:2001
Safety requirements for electrical equipment for
measurement, control, and laboratory use -- Part 1:
General requirements
EN 60825-1:1994+ A2:2001
Safety of laser products -- Part 1: Equipment
classification, requirements and user's guide
Regulatory
This device complies with Part 15 of FCC Rules. Operation is subject
to the following two conditions: (1) This device may not cause harmful
interference, and (2) This device must accept any interference received,
including interference that may cause undesired operation.
This device complies with FDA performance standards for laser
products except for deviations pursuant to Laser Notice No. 50, dated
July 26, 2001.
This Class A digital apparatus meets all requirements of the Canadian
Interference-Causing Equipment Regulation.
Cet appareil numérique de la classe A respecte toutes les exigences du
Règlement sur le matériel broullier du Canada.
appendix L | Using the GeneChip® AutoLoader
Regulatory Agency
797
Certification
AL 02 12 39816 004
92AA
See GeneChip® Scanner 3000 - AutoLoader
Specifications, on page 794.
Compliant with directive 2002/96/EC (WEEE)
Class I Laser Device
21 CFR 1040.10 and 1040.11
For Research Use Only. Not for use in diagnostic procedures.
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Affymetrix® GeneChip® Operating Software User’s Guide
Appendix
M
Data Transfer Tool Guide
Appendix
M
801
Data Transfer Tool Guide
The Affymetrix® Data Transfer Tool (DTT) provides a convenient way
to transfer data in and out of GCOS for archiving and sharing.
The DTT provides the following functionality:
• Ability to exclude DAT files
• Ability to set a variety of span file sizes to save DTT Archives
onto removable media
• Greater Backward Compatibility
• Filter data from DTT Archive or flat files for transferring IN
• Added file types for quicker archiving and unpacking
• Detection and resolution of conflicts with templates, samples, and
usersets when using DTT Archive/Flat Files
This appendix provides information about using DTT.
Using the Data Transfer Tool
To start the Data Transfer Tool:
• Click the Microsoft® Windows® Start button
and select
Programs → Affymetrix → Data Transfer Tool.
At start up, the Welcome window displays the initial options
(Figure M.1).
When working with GCOS 1.2 and higher software, the Data
Transfer Tool can be invoked from the file menus of the
applications.
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure M.1
Welcome Screen for DTT on computer with GCOS installed
GCOS SYSTEM WELCOME SCREEN
When used with a GCOS system, the DTT allows you to transfer the
following types of data:
• GCOS Data
• Mining Data stored in an AADM database
Before transferring data IN from a Mining (AADM) DTT Archive or
CAB file, you must create a new, empty mining (AADM) database in
GCOS Manager. For more information, refer to the GCOS Manager
documentation.
appendix M | Data Transfer Tool Guide
803
You can transfer data in different formats:
• DTT Archive files
• Flat Files
• CAB files
• MAS files (transfer IN only)
For more information about the different input and output data
formats, see DTT Options Dialog Box for GCOS System, on page 804.
In the Welcome page, you can:
• Select Transfer Data In or Transfer Data Out operations
• Open the DTT Options page to select input and output data
formats (see page 804)
• Review information about your system:
- Affymetrix system installed on your computer
- The system version
- System data location: The GCOS system (Local or Server) to
which the data will be transferred. When using DTT with
GCOS, use GCOS to switch between Local and Server mode.
Use the buttons at the bottom to:
Show Log
Show the log for all transfer operations.
Back
Return to the previous step (disabled in this
screen).
Next
Go to the next step.
Cancel
Close the dialog box.
Show/Hide Help
Display or conceal the Help page.
To select the operation:
1.
Select whether you want to:
- Transfer data IN to GCOS.
- Transfer data OUT of GCOS.
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Affymetrix® GeneChip® Operating Software User’s Guide
If you want to specify a file type for your transfer, click DTT
Options.
The DTT Options Page opens (see below).
3. Click Next.
The appropriate page opens.
2.
DTT Options Dialog Box for GCOS System
Click the appropriate tab to:
• Select file types for Transfer IN (see below)
• Select file types for Transfer OUT (see page 806)
DTT Options Page: Transfer IN Tab for GCOS System
The Transfer In tab allows you to choose between the following data
input formats (Figure M.2):
• DTT Archive/Flat Files: GCOS Process Data or Publish Database
contents (DTT Archive format only)
Select this option to transfer in data from DTT Archive files or flat
files. The flat files or DTT Archive file must have the associated
XML file(s) with the GCOS project and sample information. The
DAT/CEL/CHP data will be transferred into GCOS under the
appropriate project/sample and the data files will be converted to
the appropriate GCOS format.
appendix M | Data Transfer Tool Guide
805
Figure M.2
GCOS System Data Transfer Options dialog box, Transfer IN Tab
When using DTT Archive files stored on CDs, it is highly
recommended that users copy all contents of the CD to a local drive
and then import the contents.
Before transferring Mining data IN, you must create a new, empty
mining (AADM) database in GCOS Manager. For more information,
refer to the GCOS Manager documentation.
• CAB Files: GCOS Process Data or Publish Database contents
Select this option to transfer in data from CAB files. The DAT,
CEL and CHP data contained in the CAB file will be transferred to
GCOS into the appropriate project/sample in GCOS. The data will
be transferred into GCOS under the appropriate project/sample
and files will be converted to the appropriate GCOS format.
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Affymetrix® GeneChip® Operating Software User’s Guide
• Migration of Microarray Suite Data
Select this option to transfer in DAT/CEL/CHP data that do not
have the XML file with the GCOS project and sample information.
A project and sample name will have to be provided to successfully
transfer this data into GCOS. Other information required for
transfer IN will be regenerated using the information available in
the DAT/CEL headers. The data will be inserted under the user
provided project and sample name.
To select the input format:
1.
Select the radio button for the file type you wish to use.
- DTT Archive Files
- Flat Files
- CAB Files
2.
Click OK in the Data Transfer Options dialog box.
DTT Options Page: Transfer OUT Tab for GCOS System
The Transfer Out tab allows you to choose between the following data
output formats (Figure M.3):
• DTT Archive (GCOS Process Data and Publish Database
contents)
Select this option to transfer data out to flat files which are then
packaged into DTT Archive file(s). The DTT Archive file(s)
contain DAT, CEL, and CHP data files, along with an XML file
with information on the GCOS sample and project under which
the experiment was created. Use this format to preserve all GCOS
information when transferring the data. DTT Archive file options
will allow the DTT Archive file to be broken into smaller span files
if required.
DTT Archive files get a .DTT extension.
• Flat Files (GCOS Process Data only)
Select this option to transfer data out to flat files that consist of
DAT, CEL, and CHP data files, along with an XML file with
information on the GCOS sample and project under which the
appendix M | Data Transfer Tool Guide
807
experiment appears. Use this option to preserve all the GCOS
information when transferring the data from one GCOS system to
another. The XML files generated using this option have to be
transferred with the DAT, CEL and CHP data.
• CAB (GCOS Process Data and Publish Database contents)
Select this option to transfer data out to CAB files that contain the
DAT, CEL, and CHP data files, along with a text file with
information on the GCOS sample and project under which the
experiment appears. Use this option when CAB files are required
and it is necessary to preserve all the GCOS information when
transferring the data across GCOS systems.
CAB files get a .CAB extension.
Figure M.3
GCOS System Data Transfer Options dialog box, Transfer Out tab
To select the output file format:
1.
Select the radio button for the file format you wish to use.
- DTT Archive Files
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Affymetrix® GeneChip® Operating Software User’s Guide
If this file type is selected, you can choose a span file size from
the drop-down list to match the capacity of the storage media
you are using.
- Flat Files
- CAB Files
If you select CAB, you will see a dialog box (Figure M.4):
Figure M.4
Data Transfer Options dialog box, Transfer Out tab
Select the I understand DTT Archive is a better option
checkbox.
B. Click Yes.
A.
2.
Click OK in the Data Transfer Options dialog box.
TRANSFERRING DATA IN
You can use DTT to transfer Affymetrix data into the following types
of systems:
• GCOS System: Transfer data into the Process or Publish
databases.
You can transfer the following types of data into a GCOS system:
- GCOS Process data into the GCOS database
- Mining Data into an empty Publish database
- MAS 5.x data into the GCOS database
appendix M | Data Transfer Tool Guide
809
Before transferring data IN from a Mining (AADM) DTT Archive or
CAB file, you must create a new, empty mining (AADM) database in
GCOS Manager. For more information, refer to the GCOS Manager
documentation.
The system type is automatically detected by DTT.
You can transfer data archived in the following file types:
• DTT Archive files (see page 809)
• Flat files (GCOS Process data only) (see page 809)
• CAB files:
- Into a GCOS system (see page 828)
• MAS 5.x files (GCOS Process data only): Transfer individual files
(EXP, DAT, CEL, CHP) and experiment information generated
using MAS 5.x software. If the EXP file is missing, the Data
Transfer Tool will try and create an experiment file with the
available information.
For more information about importing MAS 5.x files, see
page 828.
You must select the file type for transfer on the Welcome screen.
Transferring DTT Archive/Flat File Data IN to a Computer
with GCOS
You must select the file type for transfer on the Welcome screen.
To transfer data in DTT Archive or Flat File format into a computer
with GCOS:
1.
Select data types and data for input (see page 810).
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Affymetrix® GeneChip® Operating Software User’s Guide
When using the Flat File format, you can only transfer GCOS
Process data.
Review selected data (see page 817).
3. Resolve conflicts with (GCOS Systems only):
- Templates (see page 821)
- Samples (see page 822)
- Usersets (see page 824)
2.
4.
Check that conflicts have been resolved and view the progress of
the transfer (see page 827).
Transfer DTT Archive/Flat File Data IN to GCOS: Setup
The Setup screen allows you to select DTT Archive and Flat File data
for transfer in to a computer with:
• GCOS System
You must select the file type for transfer on the Welcome screen.
When using DTT Archive files stored on CDs, it is highly
recommended that users copy all contents of the CDs to a local
drive and then import the contents.
appendix M | Data Transfer Tool Guide
811
Figure M.5
Transfer DTT Archive/Flat File Data IN to GCOS System: Setup
To set up to transfer data IN to the system:
Step 1: Select the input data location
A.
Click the Browse button and use the dialog box to select a
directory with the DTT Archive/Flat Files for transfer.
Select the Remember checkbox to make this directory the
default directory for GCOS.
If you select a directory containing a large number of DTT Archive
files, the display of the file list in the Contents of Folder list may be
delayed.
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Affymetrix® GeneChip® Operating Software User’s Guide
Step 2: Select Data Type
A.
Select the Data Type for input.
Transfer GCOS Data: transfer archived Process data.
2) Transfer Mining Data: transfer archived Mining data (only
available when used with a GCOS system).
1)
Before transferring data IN from a Mining (AADM) DTT Archive file,
you must create a new, empty mining (AADM) database in GCOS
Manager. For more information, refer to the GCOS Manager
documentation.
Step 3: Select DTT Archive/Flat data
The available DTT Archive or Flat Files are displayed in the
contents list with the following information:
File Name
Unique ID assigned to the file.
Date
Date when archive was created.
A.
Select the DTT Archive or Flat Files from the list:
❑ Click Select All to select all archives and flat data
❑ Click Clear All to clear all selections
❑ Click on File Properties to display the File Properties box
for the selected DTT Archive or Flat Files (see page 817).
Step 4: Select Experiments to Restore
Experiments in the selected DTT Archives or Flat Files are
displayed in the Experiment list with the following information:
Exp
Experiment ID
Proj
Project ID
Sample
Sample associated with the experiment.
Archive/XML
Archive/XML file containing the experiment information
A.
Select the experiments for transfer in the Experiment List.
appendix M | Data Transfer Tool Guide
813
Use the controls below the box to:
Exclude DAT data
Exclude all DAT files from the transfer process.
Clear All
Clear all selections.
Experiment
Information
Display the Experiment Information box for selected files
(see page 814).
Filter
Open the Filters dialog box (see page 815).
B.
Click Next.
❑ If you are transferring GCOS data, the Review window
open (see page 817).
❑ If you are transferring Mining data, the Select a database
dialog box opens (Figure M.6).
Figure M.6
Select a Database dialog box
This dialog box displays the available empty Mining (AADM)
databases.
Select a database to store the Mining (AADM) data from
the list in the box.
b. Click OK.
A dialog box asks for the password to the mining
database.
a.
814
Affymetrix® GeneChip® Operating Software User’s Guide
Enter the password and click OK.
The Review window opens (see page 817).
c.
Experiment Information
Figure M.7
DTT Archive Experiment Information
The Experiment Information dialog box (Figure M.7) displays the
following information:
Data Type
Type of data (dat, cel, chp).
Data Name
Identifier for the file.
Experiment
Unique ID for the associated experiment.
Number of DAT
files
Number of DAT files in the selected archive.
Number of CEL
files
Number of CEL files in the selected archive.
Number of CHP
Files
Number of CHP files in the selected archive.
Close button
Click to close the Experiment Information
box.
appendix M | Data Transfer Tool Guide
Transfer In Filters Dialog Box
To filter displayed experiments:
1.
Click the Filter button in the Setup screen (Figure M.8).
Filter button
Figure M.8
Transfer DTT Archive/Flat File Data IN to GCOS System: Setup
The Transfer In Filters dialog box opens (Figure M.9).
815
816
Affymetrix® GeneChip® Operating Software User’s Guide
Figure M.9
Transfer In Filters dialog box
2.
Select the parameters for the experiments you are interested in
from the following:
Assay Type
Type of assay performed.
Probe Array Type:
Particular probe array design used in the experiment.
User:
Person who created or imported the files.
Project
Category assigned in GCOS. Used to group a collection of
samples.
Sample
Identifier for the sample, assigned in GCOS.
Use
Use to filter using date ranges.
Experiment Date Select to filter on date experiment was created.
3.
DAT File Date
Select to filter on date DAT file associated with that
experiment was created.
From Date
Start of date range.
To Date:
End of date range.
Click Apply Filters to display data with the selected parameters;
or
Click Close to close the dialog box without applying the filters.
appendix M | Data Transfer Tool Guide
817
Properties Page
The Properties page displays additional data about the DTT Archive
or Flat File selected in the Contents list, including (Figure M.10):
• The machine on which the file was created.
• The number of experiments in the file.
• The number of span files associated with the file.
• Comments entered by the user when the file was created.
To close the Properties page:
• Click OK.
Figure M.10
File Properties page
Transfer DTT Archive/Flat Files IN to GCOS: Review Data
This screen displays a list of the files selected for transfer with
indications if there are problems (Figure M.11).
818
Affymetrix® GeneChip® Operating Software User’s Guide
Figure M.11
Data Transfer IN to GCOS System: Review Data (DTT Archive/Flat Files)
appendix M | Data Transfer Tool Guide
819
To review the data for transfer:
1.
Review the list of files for conflicts or other problems.
The Selected Item list displays the following information:
Data Type
• Project
• Sample
• Experiment
• DAT data
• CEL data
• CHP data
• GRD data
• JPG Data
with conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Data Name
ID for the file.
New Data Name
Displays the new name selected for the template, sample,
or userset during conflict resolution.
Conflict
Description of the conflict (also displayed in the Error
Description box).
2.
Click in an item row to see the full description of the problem with
a file in the Error Description box.
For more information about the error messages, see Error Messages
and Troubleshooting Guide, on page 854.
Click the Conflict Resolution Wizard button to resolve conflicts
using the wizards, if necessary (see page 820).
3.
Click Next.
The Transfer In Status window opens (see page 827).
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Affymetrix® GeneChip® Operating Software User’s Guide
Conflict Resolution Wizard
Use the Conflict Resolution Wizard to resolve problems with:
• Sample and Experiment Templates (see page 821)
Templates are predefined forms used to register samples and define
experiments in GCOS; a template has a set of attributes used to
provide information about the sample or experiment. A template
conflict arises when there are discrepancies in the number or name
of attributes used in the GCOS template and the DTT Archive/
Flat File template.
For more information about template conflicts, see Template Issues,
on page 854.
• Samples (see page 822)
Samples are created in GCOS, given attributes, and assigned to a
project and sample type. A sample conflict arises when the same
sample name exists in GCOS and in the DTT Archive/Flat file, but
the samples are assigned to different project names, sample types,
or other attributes.
For more information about sample conflicts, see Sample Issues, on
page 857.
• Usersets (see page 824)
Usersets are a set of predefined parameter settings for the analysis
algorithm. A userset conflict arises when there is discrepancy in
the parameters used in the GCOS userset and the DTT Archive/
Flat File userset.
For more information about userset conflicts, see Userset Issues, on
page 859.
The Conflict Resolution Wizard allows you to resolve these conflicts
by renaming the template, sample, or userset for the files being
transferred into GCOS using DTT.
You may need to resolve conflicts in more than one category to
transfer the data.
appendix M | Data Transfer Tool Guide
821
Resolve Templates Tab
The Resolve Templates tab allows you to resolve conflicts in templates
(Figure M.12).
A typical template conflict involves discrepancies in the attributes for
the template in the GCOS database as opposed to the template used
for the data to be imported.
Figure M.12
Conflict Resolution Wizard, Resolve Templates tab
To resolve a conflict in the templates:
A.
View the list in the Error Information box.
The Error information box displays a list of the Sample and
Experiment templates with conflicts with the following
information:
Template Name
with conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
822
Affymetrix® GeneChip® Operating Software User’s Guide
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Template Type
Can be Experiment Template or Sample Template.
Error Information
Additional information about the error (also displayed in
the box above the OK button.
For more information about template conflicts, see Template
Issues, on page 854.
Step 1: Template names can be changed using prefix/suffix or
clicking on template name.
A.
Change the template name by:
❑ Clicking on the template name in the Error Information
box and editing the name.
❑ Using the Prefix and Suffix boxes:
Enter a prefix or suffix in the appropriate box.
b. Click Rename All.
All templates in the list are renamed.
c. Click Revert All to undo the changes if necessary.
Revert All undo the changes in the template names.
Step 2: Click Resolve button to see if the conflicts are resolved.
a.
A.
Click the Resolve button and see if the error indicators in the
list disappear.
B.
Click OK to accept the changes.
Resolve Samples Tab
The Resolve Samples tab allows you to resolve conflicts between
samples in the database and in the files for transfer by renaming the
sample name for the file to be transferred (Figure M.13).
appendix M | Data Transfer Tool Guide
823
Figure M.13
Conflict Resolution Wizard, Resolve Samples tab
To resolve a conflict in the samples:
1.
View the list in the Error Information box.
Error information displays a list of the samples with conflicts with
the following information:
Sample Name
With conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Error Information
Additional information about the error (also displayed in
the box above the OK button.
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For more information about sample conflicts, see Sample Issues,
on page 857.
Step 1: Change Sample names using prefix/suffix or clicking on
template name.
A.
Change the Sample name by:
❑
❑
Clicking on the sample name in the Error Information box
and editing the name.
Using the Prefix and Suffix boxes:
Enter a prefix or suffix in the appropriate box.
b. Click Rename All.
All samples in the list are renamed.
c. Click Revert All to undo the changes if necessary.
Revert All undo the changes in the template names.
Step 2: Click Resolve button to see if the conflicts are resolved.
a.
Click the Resolve button and see if the error indicators in the
list disappear.
B. Click OK to record the changes.
A.
Resolve Usersets Tab
The Resolve Usersets tab allows you to resolve conflicts in usersets
(Figure M.14).
A typical userset conflict involves discrepancies in the parameters and
values for the userset in the GCOS database as opposed to the userset
used for the data to be imported.
appendix M | Data Transfer Tool Guide
825
Figure M.14
Conflict Resolution Wizard, Resolve Sample tab
To resolve a conflict in the userset:
1.
View the list in the Error Information box.
The Error information box displays a list of the Usersets with
conflicts with the following information:
Userset Name
With conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Error Information
Additional information about the error (also displayed in
the box above the OK button.
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Affymetrix® GeneChip® Operating Software User’s Guide
For more information about userset conflicts, see Userset Issues, on
page 859.
Step 1: Userset names can be changed using prefix/suffix or
clicking on template name.
A.
Change the Userset name by:
❑
❑
Clicking on the Userset name in the Error Information box
and editing the name.
Using the Prefix and Suffix boxes:
Enter a prefix or suffix in the appropriate box.
b. Click Rename All.
All usersets in the list are renamed.
c. Click Revert All to undo the changes if necessary.
Step 2: Click Resolve button to see if the conflicts are resolved.
a.
Click the Resolve button and see if the error indicators in the
list disappear.
B. Click OK to record the changes.
A.
appendix M | Data Transfer Tool Guide
827
Transfer DTT Archive/Flat File data In to GCOS: Transfer Data
The Transfer Data page displays the transfers in progress or completed
during this session, with basic information about the transfer
(Figure M.15).
Figure M.15
Transfer Status page (DTT Archive or flat files into GCOS system)
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The Selected Items box lists the data selected for transfer:
Data Type
• Project
• Sample
• Experiment
• DAT data
• CEL data
• CHP data
• GRD data
• JPG data
with conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Data Name
ID for the file.
Message
Status of the transfer operation.
The lower box displays the contents of the transfer log for this session.
Transferring CAB or MAS 5.x Files IN to a GCOS System
You can use DTT to transfer GCOS data, Mining data, and MAS 5.x
data in CAB or MAS 5.x format into a GCOS System.
Before transferring data IN from a Mining (AADM) CAB file, you
must create a new, empty mining (AADM) database in GCOS
Manager. For more information, refer to the GCOS Manager
documentation.
appendix M | Data Transfer Tool Guide
829
To transfer data in CAB or MAS 5.x format:
Make initial setup for transfer (see below).
2. Select data for transfer (see page 832).
3. Track progress of transfer (see page 836).
1.
You must select the file type for transfer on the Welcome screen.
Transfer CAB or MAS 5.x Files IN to GCOS System: Setup
Figure M.16
Transfer CAB files IN to GCOS system: Setup
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Affymetrix® GeneChip® Operating Software User’s Guide
To perform initial setup:
Figure M.17
Transfer MAS 5.x Data IN to GCOS System: Setup
You must select the file type (CAB or MAS 5.x) for transfer on the
Welcome screen.
Step 1: Select the input data location
A.
Click the Browse button and use the dialog box to select a
directory where the CAB or Microarray Suite 5.x data files are
located.
B.
Select the file type for input:
You cannot select a file type on the Setup screen when
importing CAB files.
appendix M | Data Transfer Tool Guide
831
The following options are used only to import MAS 5.x flat files
(.cel, .chp, and .dat):
❑ DAT - CEL - CHP: Import image data (*.DAT).
When specifying the image data, the associated experiment
information from the EXP file, the cell intensity data (CEL)
and the probe analysis data (CHP) is automatically
imported.
❑ CEL - CHP: Import cell intensity data (*.CEL) and probe
analysis data (*.CHP).
When specifying the cell intensity data (CEL), the
associated experiment information in the EXP file, the
DAT file if it is present, and probe analysis data (CHP) is
automatically imported with the cel intensity data. If the
DAT file is missing, it will be marked as archived in the
GCOS system.
Step 2: Select sample parameters
Not applicable when transferring CAB file data.
When importing MAS 5.x data:
A.
Select options for creating samples on import:
❑ Automatically create a sample for each experiment
imported.
❑ Create a single sample for all experiment files being
imported.
Enter a Sample Name or select from the drop-down list.
Only active if placing all experiments under a single sample.
C. Enter a Sample Type or select from the drop-down list.
D. Enter a Project Name or select from the drop-down list.
Step 3: Data will be stored in the following location
B.
A.
Review the GCOS database location (Local or GCOS Server)
and change if necessary.
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To change the default destination, open GCOS and select the
appropriate system (GCOS server or local system). The data
transfer tool must be closed and reopened for settings to take
effect.
You can only use the DTT to transfer MAS 5.x data into a GCOS
Workstation. You cannot use the DTT to transfer MAS 5.x data into
a GCOS Server. To transfer MAS 5.x data into a GCOS Server, use
the import functionality in GCOS Manager application.
B.
Click Next.
The Select Data screen opens (see page 832).
Transfer CAB or MAS 5.x Files IN to GCOS System: Select Data
Figure M.18
Select Data: GCOS CAB file
appendix M | Data Transfer Tool Guide
833
To select a CAB file:
1.
Select the CAB file that contains the data to be transferred from the
Select CAB files box.
To select adjacent items, press and hold the Shift key while you
click the first and last item in the selection. To select non-adjacent
items, press and hold the Ctrl key while you click the items.
You cannot select GCOS data and Mining data files for transfer in
the same operation.
This box lists the CAB files in the directory specified in Step 1 of
the Setup page. GCOS and Mining CAB files are labeled.
If you select a CAB file with GCOS data, you can review the
contents of the file in the Data: (EXPs, DATs, CELs, CHPs only)
box.
CAB files with version 4.0.0 will not contain EXP files. A version
4.0.0 CAB file containing only experiments will not have its
contents listed. To see the version of the CAB file see Step 2. The
CAB version is listed in the CAB file properties.
Keep all span files together when transferring CAB files into
GCOS.
2. Click Properties for more information about the selected CAB
file.
The Properties page opens.
3. Click Start to begin the transfer.
Follow the directions in the notice boxes that appear.
- If you are transferring GCOS data, the Transfer Data window
opens (see page 836).
- If you are transferring Mining data, the Select a database
dialog box opens (Figure M.19).
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Affymetrix® GeneChip® Operating Software User’s Guide
Figure M.19
Select database dialog box
This dialog box displays the available empty Mining (AADM)
databases.
Select a database to store the Mining (AADM) data from the
list in the box.
2) Click OK.
A dialog box asks for the password to the mining database.
1)
3)
Enter the password and click OK.
You can track the progress of the transfer in the Transfer
Data page.
appendix M | Data Transfer Tool Guide
835
To select MAS 5.x files:
Figure M.20
Select Data: MAS 5.x file
Select the MAS 5.x files that you wish to transfer from the Select
files box.
To select adjacent items, press and hold the Shift key while you
click the first and last item in the selection. To select non-adjacent
items, press and hold the Ctrl key while you click the items.
To select all files in the box, click Select All.
To clear all selections, click Clear All.
2. Click Start to begin the transfer.
Follow the directions in the notice boxes that appear.
The Transfer Data window opens.
1.
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Affymetrix® GeneChip® Operating Software User’s Guide
Properties Page
Figure M.21
Properties Page
The Properties page (Figure M.21) displays additional data about a
GCOS CAB file selected in the Select page, including:
• The machine on which the CAB file was created.
• The number of experiments in the GCOS CAB file.
• The number of span files associated with the CAB file. Span files
are automatically created when the CAB file size exceeds 2 GB.
Keep all span files together when transferring CAB files into
GCOS.
• Comments entered by the user when the CAB file was created.
To close the Properties page:
• Click OK.
Affymetrix Data Transfer Tool: Transfer Data
The Transfer Data page displays the transfers in progress or completed
during this session, with basic information about the transfer.
The progress bar (displayed only for transfers with CAB files) shows
the progress of the transfer taking place.
appendix M | Data Transfer Tool Guide
837
Figure M.22
Transfer Data, transferring Mining Data from CAB file IN to GCOS
TRANSFERRING DATA OUT
You can use the DTT to transfer the following types of data out of
GCOS:
• GCOS Process data
• Mining Data
You can transfer data out of GCOS in the following formats:
• DTT Archive (see page 838)
• Flat File (GCOS Process data only) (see page 838)
• CAB files (see page 846)
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For more information about selecting file types for data transfer, see
DTT Options Dialog Box for GCOS System, on page 804.
You cannot use DTT to transfer data out of a computer unless GCOS
is installed.
You must select the file type for transfer on the Welcome screen.
Transferring Data OUT in DTT Archive and Flat Files
To transfer data OUT in DTT Archive and Flat Files:
Set up the transfer (see page 839).
2. Select the actual data to be transferred (see page 841).
3. Review the data that will be transferred to the CAB file
(see page 844).
4. Observe the progress of the transfer on the Transfer Data page
screen (see page 844).
1.
You must select the file type for transfer on the Welcome screen.
appendix M | Data Transfer Tool Guide
839
Data Transfer Out of System: Setup (DTT Archive and Flat Files)
Figure M.23
Data Transfer OUT of System: Setup (DTT Archive/Flat Files)
You must select the file type for transfer (DTT Archive or Flat File)
on the Welcome screen.
To set up a data transfer OUT:
Step 1: Select Data Type
A.
Select the data type for transfer:
❑ Transfer GCOS Data: transfer data from GCOS Process
Database.
❑ Transfer Mining Data: transfer data from Mining (AADM)
database (option not available when using Flat File format).
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Affymetrix® GeneChip® Operating Software User’s Guide
Selecting Transfer Mining Data will export the entire contents of
the selected Mining (AADM) database.
Step 2: Select the filters
These controls are active only if you are transferring GCOS data.
A.
Select the filters for the data displayed in the Data Select screen:
Assay Type
Type of assay performed
Probe Array Type:
Particular probe array design used in the experiment.
User:
Person who created or imported the files.
Project
Category assigned in GCOS. Used to group a collection of
samples.
Sample
Identifier for the sample, assigned in GCOS.
Select Date Filter
Use to filter using date ranges.
Experiment Date Select to filter on date experiment was created.
DAT File Date
Select to filter on date DAT file associated with that
experiment was created.
From Date
Start of date range.
To Date:
End of date range.
Only data that matches the parameters selected here is
displayed in the Select Data screen (Figure M.24).
Step 3: Data will be retrieved from the following location
A.
Review the location of the data source and change if necessary.
To change the location of the data source (GCOS local or GCOS
Server) open GCOS and change the option in the default
settings for the application. The Data Transfer Tool must be
closed and reopened for settings to take effect.
appendix M | Data Transfer Tool Guide
B.
841
Click Next.
The Select Data page opens (see below).
Data Transfer Out of System: Select Data (DTT Archive and Flat
Files)
Figure M.24
Data Transfer OUT of System: Select Data (GCOS data)
To transfer GCOS data:
Step 1: Select Data to transfer OUT
Select the type of data to display using the Display All dropdown box.
B. Select the data in the Select Data box.
❑ Click Clear All to clear previous selections.
❑ Click Select All to select all data shown on the screen.
A.
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The data copied to the archive file set is different for some of the
data selections:
❑ Project: For each selected project, the sample, experiment,
and all DAT, CEL, and CHP data, is copied to the archive
file set with the Project data.
❑ Sample: For each selected sample, the parent project of the
sample and all experiment(s), DAT, CEL, and CHP data
under the sample, is copied to the archive file set with the
Sample data.
❑ Experiment: For each selected experiment, the parent
project and sample of the experiment and all DAT, CEL,
and CHP data under the experiment, is copied to the
archive file set with the Experiment data.
❑ DAT Data: For each selected DAT, the parent project,
sample, and experiment of the DAT data is copied to the
archive file set file with the DAT data. CEL and CHP data
is not copied.
❑ CEL Data: For each selected CEL, the parent project,
sample, experiment, and DAT dat of the CEL data, is
copied to the archive file set with the CEL data. CHP data
is not copied.
❑ CHP Data: For each selected CHP, the parent project,
sample, experiment, DAT, and CEL data is copied to the
archive file set with the CHP data.
Step 2: Include DAT Data
Choose whether to include or exclude the DAT data (option not
available for transferring mining (AADM) data).
Step 3: DTT Archive/Flat File Information
A.
A.
Enter a location, file name, and comments for the archive file
set that will be created.
appendix M | Data Transfer Tool Guide
843
This step is disabled when transferring data to Flat Files.
B.
Click Review to review the data that will be transferred into
the archive file set.
C.
Click Start to begin the transfer.
Follow the directions in the notice boxes that appear.
Figure M.25
Data Transfer OUT of System: Select Data (Mining (AADM) data)
To transfer Mining Data:
Certain options are disabled in this screen when transferring Mining
(AADM) data.
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Step 1: Select Data to Transfer OUT
The Display All drop-down list is disabled when working with
Mining Data.
Select the Mining (AADM) database in the Select Data box.
Step 2: Include DAT Data
A.
The Step 2: Include DAT Data option is not active when transferring
Mining (AADM) data.
Step 3: DTT Archive/Flat File Information
A.
Enter a location, file name, and comments for the DTT Archive
file or the XML file for the flat files to be created.
B.
Click Review.
The Enter Password DB opens (Figure M.26).
Figure M.26
Enter Password dialog box
C.
Enter the password for the selected database and click OK.
The Data Transfer Out of System: Review Data window opens
(see page 844).
Transferring Data Out of System: Review Data (DTT Archive and
Flat File)
The Review Data page allows you to review the data selected for the
DTT Archive or Flat File.
appendix M | Data Transfer Tool Guide
845
To review the data chosen for transfer:
1.
Review the Selected Items list:
Data Type or
Mining Database
• Project
• Sample
• Experiment
• DAT data
• CEL data
• CHP data
• GRD data
• JPG Data
with conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
2.
Data Name
Data type (see list above).
Message
Error or warning message
Size Estimate (MB)
Estimate of the necessary disc space in megabytes.
Error Description
Details of the detected problem, if any.
Click Next to continue the transfer
The Transfer Data page opens.
Affymetrix Data Transfer Tool: Transfer Data (DTT Archive and
Flat Files)
The Transfer Data page displays the transfers in progress or completed
during this session, with basic information about the transfer.
The Selected Items box lists the data selected for transfer:
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Data Type
• Project
• Sample
• Experiment
• DAT data
• CEL data
• CHP data
• GRD data
• JPG Data
with conflict indicators:
Data cannot be transferred due to conflict with template,
sample, or userset or other problem.
Data can be transferred.
Transfer with warning: Data can be transferred but
problems exist (may overwrite existing data, etc.).
Data Name
ID for the file.
Message
Status of the transfer operation.
The lower box displays the contents of the transfer log for this session.
Transferring Data OUT in CAB Files
To transfer data OUT of GCOS to a CAB file:
Set up the transfer (see page 847).
2. Select the actual data to be transferred (see page 849).
1.
Review the data that will be transferred to the CAB file
(see page 852).
4. Observe the progress of the transfer on the Transfer Data page
screen (see page 836).
3.
You must select the file type for transfer on the Welcome screen.
appendix M | Data Transfer Tool Guide
847
Data Transfer Out of System: Setup (CAB)
Figure M.27
Data Transfer OUT of System: Setup (CAB)
You must select the file type for transfer on the Welcome screen.
To set up a data transfer OUT into CAB format:
Step 1: Select Data type
A.
Select the data type for transfer:
❑ Transfer GCOS Data: transfer data from GCOS Process
Database.
❑ Transfer Mining Data: transfer data from Mining (AADM)
database.
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Selecting Transfer Mining Data will export the entire contents of
the selected Mining (AADM) database.
Step 2: Select the Filters
A.
Select the filters for data displayed in the next screen.
These controls are active only if you are transferring GCOS data.
You can filter using the following parameters:
Assay Type
Type of assay performed.
Probe Array Type
Particular probe array design used in the experiment.
User
Person who created or imported the files.
Project
Category assigned in GCOS. Used to group a
collection of samples.
Sample
Identifier for the sample, assigned in GCOS.
Date
Data created during a range of dates:
From
Start date.
To
End date.
Step 3: Data will be retrieved from the following location
Review the data location.
To change the location of the data source (GCOS local or GCOS
Server) open GCOS and change the option in the default
settings for the application. The Data Transfer Tool must be
closed and reopened for settings to take effect.
B. Click Next.
The Select Data page opens.
A.
appendix M | Data Transfer Tool Guide
849
Data Transfer out of System: Select Data (CAB)
Figure M.28
Data Transfer OUT of System: Select Data (CAB)
To select GCOS Data for transfer:
Step 1: Select Data to transfer OUT
Select the type of data to display using the Display All dropdown box.
B. Select the data in the Select Data box.
❑ Click Clear All to clear previous selections.
❑ Click Select All to select all data shown on the screen.
The data copied to the CAB file is different for some of the data
selections:
A.
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Affymetrix® GeneChip® Operating Software User’s Guide
❑
❑
❑
❑
❑
❑
Project: For each selected project, the sample, experiment,
and all DAT, CEL, and CHP data, is copied to the CAB file
with the Project data.
Sample: For each selected sample, the parent project of the
sample and all experiment(s), DAT, CEL, and CHP data
under the sample, is copied to the CAB file with the
Sample data.
Experiment: For each selected experiment, the parent
project and sample of the experiment and all DAT, CEL,
and CHP data under the experiment, is copied to the CAB
file with the Experiment data.
DAT Data: For each selected DAT, the parent project,
sample, and experiment of the DAT data is copied to the
CAB file with the DAT data. CEL and CHP data is not
copied.
CEL Data: For each selected CEL, the parent project,
sample, experiment, and DAT dat of the CEL data, is
copied to the CAB file with the CEL data. CHP data is not
copied.
CHP Data: For each selected CHP, the parent project,
sample, experiment, DAT, and CEL data is copied to the
CAB file with the CHP data.
Step 2: Include DAT Data
Choose whether to include or exclude the DAT data (option not
available for transferring mining (AADM) data).
Step 3: CAB Information
A.
A.
Enter a location, file name, and comments for the CAB file that
will be created.
B.
Click Review to review the data that will be transferred into
the CAB file.
appendix M | Data Transfer Tool Guide
851
To select Mining Data for transfer:
Selecting Transfer Mining Data will export the entire contents of the
selected Mining (AADM) database.
Certain options are disabled in this screen when transferring Mining
(AADM) data.
Step 1: Select Data to Transfer OUT
The Display All dropdown list is disabled when working with
Mining Data.
Select the Mining (AADM) database in the Select Data box.
Step 2: Include DAT Data
A.
The Step 2: Include DAT Data option is not active when transferring
Mining (AADM) data.
Step 3: CAB Information
A.
Enter a location, file name, and comments for the CAB file that
will be created in Step 3.
B.
Click Review
The Enter Password DB opens (Figure M.29).
Figure M.29
Enter Password dialog box
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Affymetrix® GeneChip® Operating Software User’s Guide
C.
Enter the password for the selected database and click OK.
The Data Transfer Out of System: Review Data window opens
(see below).
Transferring Data Out of System: Review Data (CAB)
Figure M.30
Data Transfer OUT of System: Review Data (CAB)
The Review Data page allows you to review the data selected for the
CAB file.
When transferring GCOS data, the page lists any of the following data
types that have been selected:
• Project
• Sample
• Experiment
appendix M | Data Transfer Tool Guide
853
• DAT data
• CEL data
• CHP data
• GRD data
• JPG data
When transferring mining data, the page lists the selected mining
(AADM) databases.
• Click Start to begin the transfer and go to the Transfer Data page
(see page 836).
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Error Messages and Troubleshooting Guide
Error messages appear in DTT when there is a conflict of some sort
between the data being imported and the existing contents of the
GCOS databases. Many of these conflicts can be resolved using the
Conflict Resolution Wizard (see Conflict Resolution Wizard, on
page 820). Other problems may require other action to resolve.
Error messages describe:
• Template Issues (see below)
• Sample Issues (see page 857)
• Userset Issues (see page 859)
• Miscellaneous Issues (see page 860)
TEMPLATE ISSUES
Templates are predefined forms used to register samples and define
experiments in GCOS; a template has a set of attributes used to
provide information about the sample or experiment. A template
conflict arises when there are discrepancies in the number or name
of attributes used in the template in GCOS and the template in the
DTT Archive/Flat File.
For more information about resolving template conflicts, see
Resolve Templates Tab, on page 821.
appendix M | Data Transfer Tool Guide
855
Table M.1
Template issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
Sample Template [<Name of
sample template>] cannot be
restored because the template
already exists in GCOS but has
different template attributes. Extra
attribute(s): <Name of attribute>
The sample template to be
transferred IN with the sample
already exists in GCOS. The
sample template attributes are
different. The extra attribute in the
sample to be transferred IN is
called <Name of attribute>
This message will also apply to
experiment templates.
Use the Conflict Resolution
Wizard to rename the template to
be transferred in.
As an alternative, add the attribute
that is displayed in the error
message into the template
already in GCOS.
Sample Template [<Name of
template>] cannot be restored
because the template already
exists in GCOS but has different
template attributes. Data type
mismatch for attribute(s): <Name
of attribute>
The sample to be transferred In
and the sample in GCOS use a
template with identical names and
attributes.
However, the data type (string,
integer, float, integer etc.) for the
listed attribute is different when
comparing the two templates.
This message will also apply to
experiment templates.
Use the Conflict Resolution
Wizard to rename the template to
be transferred in.
Sample Template [<Name of
template>] cannot be restored
because the template already
exists in GCOS but has different
template attributes. Controlled
values mismatch for attribute(s):
<Name of attribute>
The sample to be transferred In
and the sample in GCOS use a
template with identical names and
attributes.
Use the Conflict Resolution
Wizard to rename the template to
be transferred in.
However, the listed attribute is a
controlled attribute that uses
different control values when
compared with the controlled
values used by the template
attribute in GCOS.
This message will also apply to
experiment templates.
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Table M.1
Template issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
Warning: Sample Template
[<Name of template>] will not be
restored because the template
already exists in GCOS but the
template attributes are in different
order. Restored sample will use
the existing template in the GCOS.
This is only a warning. The
attribute order used by the
incoming template is different
than the attribute order of the
template already in GCOS.
No further action is required.
Warning: Sample Template
[<Name of sample template>]
already exists in GCOS but the
template in the DTT Archive
contains more template
attributes. The extra attributes will
be inserted into the existing
template in GCOS. Extra
attribute(s): <Name of attribute>.
This is a warning or an error based
on the user rights. It indicates that
the template to be transferred in
with the data already exists in
GCOS. The template in GCOS has
fewer attributes than the one
being transferred IN. The GCOS
template will be updated with the
new attributes if the user has
rights to update the template in
the database. On a GCOS Server,
this may show up as an error if the
user does not have rights to the
update the template.
This message will also apply to
experiment templates.
When this is displayed as a
warning, no further action is
required.
Failed to restore experiment
[<Name of experiment>] because
there are errors in restoring the
associated experiment template
[<Name of experiment
template>].
This error is displayed when the
software fails to transfer IN the
experiment template. All
experiments using this template
and all children of the
experiment(s) will fail to transfer
IN.
Use the Conflict Resolution
Wizard to rename the template to
be transferred in.
This message will also apply to
experiment templates.
This message will shows up as an
error when transferring data IN to
a GCOS Server and if the user
does not have permission to
maintain templates. To resolve
this, use the conflict wizard to
rename the template and bring it
in as a new template. Alternately,
speak with your GCOS Server
administrator to get the
appropriate permission to
maintain templates on the server.
This can be done by the
administrator using the roles tab
in GCOS Manager.
appendix M | Data Transfer Tool Guide
857
SAMPLE ISSUES
Samples are created in GCOS, given attributes, and assigned to a
project and sample type. A sample conflict arises when the same
sample name exists in GCOS and in the DTT Archive/Flat file, but
the samples are assigned to different project names, sample types,
or other attributes.
For more information about resolving sample conflicts, see Resolve
Samples Tab, on page 822.
Table M.2
Sample issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
The sample already exists in
GCOS but has different sample
types. The sample type in the DTT
Archive is [<sample type value of
Sample to transfer IN>] but the
one in GCOS is [<sample type
value of sample in GCOS>].
The “sample type” field for
sample associated with the
experiment to be transferred IN
has a different value than the one
used by the sample with the same
name in GCOS.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred in. As an alternative,
open up the experiment in GCOS
UI and change the sample type
value to be the same as that used
by the sample to be transferred
IN.
The sample already exists in
GCOS but has different project
names. The project name in the
DTT Archive is [<Project value of
sample to transfer IN>] but the
one in GCOS is [<Project value of
sample in GCOS>].
The “Project” field for sample
associated with the experiment to
be transferred IN has a different
value than the one used by the
sample with the same name in
GCOS.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred IN.
As an alternative, open up the
experiment in GCOS UI and
change the “Project” attribute
value to be the same as that used
by the Sample to be transferred
IN.
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Affymetrix® GeneChip® Operating Software User’s Guide
Table M.2
Sample issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
The sample already exists in
GCOS but has different project
names and sample types. Project
name is [<Project value of sample
to transfer IN>] and sample type is
[<sample type value of Sample to
transfer IN>] for the sample in the
DTT Archive but [<Project value of
sample in GCOS>] and [<sample
type value of sample in GCOS>] in
GCOS respectively.
The “sample type” and “Project”
value for the sample associated
with the experiment to be
transferred IN has a different
value than the one used by the
sample with the same name in
GCOS.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred in.
As an alternative, open up the
experiment in GCOS UI and
change the “sample type” and
“Project” value to be the same as
that used by the sample to be
transferred IN
The sample already exists in
GCOS but has different sample
attribute value. The attribute that
have different values is <name of
attribute>.
A sample using the same name as
the one to be transferred IN
already exists in GCOS and uses
the same template as the sample
to be transferred IN. The sample
template attribute value in the
sample to be transferred IN does
not match up with the sample
template attribute value already in
GCOS.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred in.
The sample already exists in
GCOS but the two sample use
templates with different names.
A sample using the same name as
the one to be transferred IN
already exists in GCOS. The two
samples use a different sample
template.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred in.
The sample already exists in
GCOS but has different number of
sample attributes. The sample in
the DTT Archive has 3 attributes
but the one in GCOS has 4.
A sample using the same name as
the one to be transferred IN
already exists in GCOS. The two
samples use templates with
identical names. However the
number of template attributes
used by the sample in GCOS is
different than the sample in the
DTT Archive.
Use the Conflict Resolution
Wizard to rename the sample
used by the experiment to be
transferred in.
appendix M | Data Transfer Tool Guide
859
USERSET ISSUES
Usersets are a set of predefined parameter settings for the analysis
algorithm. A userset conflict arises when there is discrepancy in
the number and values of parameters used in the GCOS userset and
the userset in the DTT Archive/Flat File.
For more information about resolving userset conflicts, see Resolve
Usersets Tab, on page 824.
Table M.3
Userset Issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
Userset [<Name of the userset>]
cannot be transferred IN because
the user does not have the
appropriate privilege to create/
update usersets. Please use the
roles tab in GCOS Manager to get
the necessary privilege.
This is an error that will be
displayed when transferring IN
data onto a GCOS Server and the
user does not have permission to
transfer in Usersets.
This message will shows up as an
error when transferring data IN to
a GCOS Server and if the user
does not have permission to
maintain userset. To resolve this,
use the conflict wizard to rename
the userset and bring it in as a
new userset.
As an alternative, speak with your
GCOS Server administrator to get
the appropriate permission to
maintain usersets on the server.
This can be done by the
administrator using the roles tab
in GCOS Manager.
Userset [<Name of userset>]
cannot be restored because the
userset already exists in GCOS
but has different parameter sets
and/or attributes mismatched.
<Name of parameter>
This is an error that will be
displayed when the user tries to
transfer in a userset that already
exists in the GCOS database. The
userset parameters for the array
do not match.
Use the Conflict Resolution
Wizard to rename the userset to
be transferred in.
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Table M.3
Userset Issues
Error Message
Why the Transfer IN is flagged
as an error
How to resolve the error
Warning: Userset [<Name of
userset>] already exists in GCOS
but the userset in the DTT Archive
contains more parameter sets.
The extra parameter set will be
inserted into the existing userset
in GCOS. <Name of
parameterset>
This is a warning or an error
based on create/update
permissions. The message will be
displayed when the user tries to
transfer in a userset that contains
more parametersets than the
userset in GCOS. The extra
userset will be inserted into GCOS
if the user has appropriate
permissions.
When this is displayed as a
warning, no further action is
required.
This message will shows up as an
error when transferring data IN to
a GCOS Server and if the user
does not have permission to
maintain usersets. Speak with
your GCOS Server administrator
to get the appropriate permission
to create/maintain usersets on the
server. This can be done by the
administrator using the roles tab
in GCOS Manager.
This userset uses multiple probe
arrays one of which is <Name of
userset>. Probe array type
<[Name of userset not installed in
GCOS]> is not installed on the
system. Please reinstall this probe
array on your system and retry the
transfer IN.
This is an error when the user is
trying to transfer IN an
experiment that uses a userset
and the incoming Userset has
multiple probe arrays, one of
which is not installed on the
system. The software will not
transfer IN the experiment if this
probe array has not been installed
on the system.
Resolve by installing the library
for the probe array type the name
of which is given in the error
message.
MISCELLANEOUS ISSUES
The following error messages appear for miscellaneous issues that can
cause problems transferring data IN to GCOS.
appendix M | Data Transfer Tool Guide
861
Table M.4
Miscellaneous Issues
Error Message
Why the Transfer IN is
flagged as an error
How to resolve the error
Probe array type [<name of probe
array>] is not installed on the system.
Experiment [<Name of experiment>]
cannot be restored.
This message is displayed
when trying to transfer IN
an experiment for which
the probe array does not
exist on the local system.
Install the library file for the probe
array specified in the error message.
Experiment already exists in GCOS
database
This is an error message
displayed when an
experiment name in GCOS
conflicts with an
experiment to be
transferred IN.
GCOS can have only 1 experiment
with the same name in the database.
Use GCOS Manager to delete the
experiment in GCOS to transfer IN
the experiment from the archive.
Failed to restore experiment [<Name
of experiment>] because there are
errors in restoring the associated
experiment template [<Name of
experiment template>].
This error is displayed
when the software fails to
transfer IN the experiment
template. All experiments
using this template and all
children of the
experiment(s) will fail to
transfer IN.
Use the Conflict Resolution Wizard to
rename the template to be
transferred in.
Hybridization protocol script [<Name
of script>] is not installed on the
system. The protocol parameter will
not be restored.
This is a warning
indicating that the
parameters from the wash
and stain script will not be
inserted into the GCOS
database because the
fluidics script has not been
installed using the script
installer.
The wash and stain scripts can be
installed using the appropriate
fluidics script installer. Once the
script is installed, the parameters will
be restored when the experiment is
transferred IN.
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Affymetrix® GeneChip® Operating Software User’s Guide
Table M.4
Miscellaneous Issues
Error Message
Why the Transfer IN is
flagged as an error
How to resolve the error
Failed to transfer data file [<Name of
file>] which already exists in the
GCOS database.
This message is displayed
if the data file is associated
with an experiment in the
database. The experiment
name in GCOS database is
different than the
experiment name in the
data to be transferred IN.
However, the children of
the experiment to be
transferred IN, clash with
datafiles with the same
name in the GCOS
database.
It will not be possible to transfer IN
the data files without first deleting
the data files in GCOS. Use GCOS
Manager to delete the files in the
database if they are no longer
required.
Data file [<Name of file>] cannot be
transferred because the associated
parent data file [<Name of parent>]
cannot be transferred.
This message will be
displayed for all children of
a GCOS object that will has
an error. E.g. If an
experiment has an error
icon next to it, all children
of the experiment (DAT,
CEL and CHP) will have this
error message.
If a CHP file uses a userset
and the userset cannot be
transferred IN, the CHP file
will fail to transfer IN.
Use the Conflict Resolution Wizard to
resolve templates, samples and
usersets.
If the parent is an experiment, the
error is displayed if the experiment
already exists in the database.
Warning: Data file [<Name of data
file>] already exists in GCOS data
folder. The data file will be
overwritten.
This is a warning. This
indicates that there is a file
in the GCOS data directory
that will be overwritten.
This applies to JPG and
GRD files. It will also apply
the DAT, CEL and CHP files
when the files are not
associated with any
experiment in the GCOS
database.
Move the files out of the data
directory if they need to be
preserved.
appendix M | Data Transfer Tool Guide
863
Table M.4
Miscellaneous Issues
Error Message
Why the Transfer IN is
flagged as an error
Warning: Experiment file [<Name of
EXP file>] already exists in the <Name
of directory>. The experiment file will
be overwritten.
This message will show up
on MAS 5.x systems when
the experiment to be
transferred IN already
exists.
How to resolve the error
Move the experiment file out of the
data directory if they need to be
preserved.
Parsing Failures and Character Issues
The DTT Archive and Flat File formats use XML files for the
experiment information that DTT uses to import the data. When the
XML file contains characters that can’t be parsed by the XML parser,
DTT gives the following error message (Figure M.31):
Figure M.31
XML Parsing Error message
When the error appears, you need to create a DTTConfig.CSV
mapping file that provides the correct ASCII decimal code for the
character, so DTT can use the mapping file to parse the XML file.
To create the DTTConfig.CSV mapping file:
1.
Determine which character is causing the problem in the XML
file.
The most likely source of the invalid character is the experiment
name, sample name, or one of the sample/experiment template
attribute values. If you have used a non-US English symbol, then
the non-US english symbol would need to be changed to an ASCII
representation.
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Affymetrix® GeneChip® Operating Software User’s Guide
GCOS has only been validated on a U.S.English environment.
2.
Determine the ASCII decimal character code for that character.
You can use the Symbol dialog box to find the ASCII decimal
character code:
Open a document in Microsoft® Word.
B. Select Insert → Symbol from the Word menu bar.
The Symbol dialog box opens (Figure M.32).
A.
Figure M.32
Symbol dialog box in Microsoft Word
Select Normal Text for the font
D. Select the symbol causing the problem in the list.
E. Select ASCII (decimal) in the From drop-down box.
C.
Note the ASCII character code
3. Create the DTTConfig.CSV character mapping file.
F.
appendix M | Data Transfer Tool Guide
865
The DTTConfig.CSV file (Figure M.33) is a comma separated
value file.
Figure M.33
.CSV file
It contains a line for each character that needs the special mapping
to ASCII code in the format: symbol, ASCII decimal
code.
You can use any text-editing program, such as Notepad, to create
the file.
4.
Place the .CSV file in the same directory as the DTT executable.
DTT will use the character mappings to parse the XML files.
DTT 1.1 can parse the following characters without a .CSV file:
&, <, >,°, ®, £, ¥
GCOS Data Compatibility Table
GCOS software is backwards compatible. This means data generated
with previous versions of GCOS or MAS 5.x software can be read with
the latest version of GCOS. Data in CAB files is converted only when
transferring data generated on GCOS systems into a system with
Microarray Suite 5.x or when transferring data generated on GCOS 1.2
or later versions into GCOS 1.0/1.1/1.1.1.
The data compatibility table gives additional information about the
types of data transfers that are possible.
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Affymetrix® GeneChip® Operating Software User’s Guide
Any experiments using probe array types that require sub-gridding
on DAT images will not be restored to GCOS versions 1.2 and lower.
This includes Microarray Suite Software.
Table M.5
Data compatibility table
Target system
Data format in CAB file
Comments
Microarray Suite 5.0
The CEL and CHP data formats
were updated in GCOS 1.x. CEL
and CHP Data generated on
GCOS 1.x systems will be
converted to the MAS 5.0 format.
The software will copy the DAT
data if they were transferred to
the CAB file during the CAB
creation process.
Data generated on a GeneArray® 2500 scanner
can be transferred to a MAS 5.0 system. Data
acquired from all other scanners will be rejected.
Only expression and universal assay data can be
transferred into a system with MAS 5.0.
CEL data for the associated CHP data is required
to convert CHP data from a GCOS system to a
MAS 5.x system.
The Data Transfer tool is not supported on
Microsoft® Windows® NT SP6a systems.
Microarray Suite 5.1
The CEL and CHP data formats
were updated in GCOS 1.x. CEL
and CHP Data generated on
GCOS systems will be converted
to appropriate formats. The
software will copy the DAT data
if they were transferred to the
CAB file during the CAB creation
process.
Data generated using the GCS 3000 High
Resolution scanner cannot be transferred to a
MAS 5.1 system.
CEL data for the associated CHP data is required
to convert CHP data from a GCOS system to a
MAS 5.x system.
Only expression and universal assay data can be
transferred into a system with MAS 5.1.
appendix M | Data Transfer Tool Guide
867
Table M.5
Data compatibility table
Target system
Data format in CAB file
Comments
GCOS 1.0/1.1/1.1.1
The CHP data format was
updated going from GCOS 1.0/
1.1/1.1.1 to GCOS 1.2 or later.
CHP data generated on GCOS 1.2
or later will be converted to the
appropriate GCOS 1.0/1.1/1.1.1
format.
GCOS software is backwards
compatible. All data which was
generated on a Microarray Suite
5.x system will be copied without
any conversion.
Expression, Mapping, Universal and
Resequencing data can be transferred between
the two GCOS systems. CHP data generated
using the new Dynamic Model Mapping
algorithm cannot be transferred to a GCOS 1.0/
1.1/1.1.1 system because the software does not
support the new algorithm.
CEL data for the associated CHP data is required
to transfer CHP data from a GCOS 1.2 or later
system to a GCOS 1.0 or MAS 5.x system.
Data from GCOS 1.3 and higher systems that use
sub-grids cannot be transferred to a GCOS 1.0/
1.1/1.1.1/1.2 system
GCOS 1.3
New algorithms to support data
that require sub-grids were
introduced in GCOS 1.3. In
addition when a DAT file is
created, a JPG representation of
the same file is created
automatically. These files cannot
be transferred to a GCOS system
with version less than 1.3.
GCOS 1.4
The CHP data format for
CustomSeq arrays was updated
going into GCOS 1.4. This data
will lose new fields if transferred
back to older systems that do not
support the resequencing
format.
System without any
Affymetrix Software.
When transferring CAB data into
systems without any Affymetrix
software, all data is converted
into GCOS 1.1.1 format.
Before extracting CHP data from the CAB files, it
is necessary to copy the library (*CDF) files into
the target directory.
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Affymetrix® GeneChip® Operating Software User’s Guide
Index
871
Index
Symbols
indicator lights 737
manual mode 777
Microsoft Exchange 741
regulatory 796
scanning a probe array 751–
786
setting up 732
SMTP 743
specifications 794
stopping a scan 782
troubleshooting 787
.CSV file 863
for character mapping 864
A
Act as Part of the Operating
System policy 612
Affymetrix Technical Support 6
algorithm
Alignment 147
Cell Summary Report 679
Expression 45
empirical 638
statistical 636
expression 627
Alignment algorithm 147
alignment, grid 147
alignment, main grid 154
alignment, subgrid 162
alpha1 678
alpha2 678
amino acid codes 691
Analysis and Transfer Status
window 133
analysis information 253
automode 771
avg diff
empirical analysis 640
avg diff change
empirical analysis 643
B=A
empirical analysis 643
background subtraction 629
barcode 754
barcodes 80, 83, 109, 124, 125
baseline data 674
batch analysis
renaming results 306–308
resuming 309
running 309
selecting baseline 303
selecting userset 302
analysis information table 243
exporting 244
Analysis Service 598
analysis settings 335
archiving data 359–361
attributes 439
activate in template 440
deactivate in template 440
edit in template 441
insert in template 440
Batch Analysis window 298
removing data 308
toolbar 698
batch file
exporting 309
importing 310
bookmarks
creating 213
editing 214
viewing 214
AutoLoader 731–797
AC power connection 732
disabled 784
email system 739
Ethernet connection 732
computing 195
image settings 196–204
recalculating 196
Cell Summary Report 178
algorithm 679
for Expression arrays 181
for Mapping arrays 181
for Resequencing arrays 186
generating 178
change 628
change p-value 628
client software
B
exporting 244
call 631
carousel 767, 769
CE Mark Declaration of Conformity 583
cell coordinates 329
cell intensity data 44
C
CAB files (DTT) 807
testing
DMT 518
GCOS Manager 471,
523
troubleshooting
GCOS 716
GCOS Manager 721
codes
amino acid 691
IUPAC base 691
columns
resizing, hiding, or reordering 706
comparison analysis results
empirical algorithm 641
statistical algorithm 637
comparison expression analysis 229–230, 235–242, 633
selecting baseline 236
configure
data storage 55
fluidics station 74
scanner 75
872
controls
Affymetrix® GeneChip® Operating Software User’s Guide
defaults
See expression report controls.
CustomSeq for Resequencing
arrays
aligning subgrids 172
D
data
archiving 359–361
exporting 368
filtering 71–73
opening 69
unarchiving 361
viewing information 69
Data Mining Tool
analysis settings 335
image settings 328–333
Defaults dialog box
Database tab 55
descriptions 251
detection 628, 630
detection p-value 628
difference call
empirical analysis 642
discrimination value 631
documentation
conventions used 3
online 5
domain user requirements
for GCOS Services 588
installing 531–538
data ownership 363
assign 363
assume 363
DPos-DNeg ratio
empirical analysis 642
DTT 801
error messages 854
data storage
configure 55
DTT Archive file
format 806
Data Transfer Tool
see DTT
data tree 64
DTT CAB files 807
DTT flat files
format 806
display options 66
shortcut menu 66
data types 68
experiment data 686
fluidics protocols 685
probe information 685
database
change password 461
gene information 47
process 47
publish 47
database (workstation)
relocate 466
database setting 55
dec ratio
empirical analysis 641
decrease
empirical analysis 641
E
editing
experiment information 85
expression report 192, 291
empirical algorithm
metrics 638
Entrez 252
error message
DTT 854
error messages 789
experiment
defining 80
renaming 67
experiment data
publishing 46
experiment information
editing 85
viewing 85
Experiment Information Window 758
experiment setup 41
exporting data 368
analysis information 244
batch file 309
metrics table 246–249
expression algorithm 627
expression analysis 45
analysis information 253
analysis information table
243
exporting 244
comparison 229–230, 235–
242
selecting baseline 236
graphs
intensity bar graph 279
scatter graph 260
series graph 274, 279
measured images 257
metrics table 245, 246
report 283–289
settings 231
single-array 226–228, 232–
234
expression analysis settings
baseline 674
normalization 655
probe masks
scaling 645
user-modifiable parameters
677
Expression Analysis window
(EAW) 46, 242
expression report 283–289
controls 290
editing 192, 291
find feature 192, 291
generating 178, 284
parameters 181, 186, 287–
289
Index
printing 343
settings 180, 285
Publish tab 381
Roles tab 441
starting 347
Template tab 425
troubleshooting 721
Userset tab 415
F
filter samples
process tab 380
filters 71–73
find feature 253
expression report 192, 291
probe set information 253
GCOS Server
checking database setting 55
GCOS server
register 369, 460
unregister 371, 460
view events 371
view publish tasks 372
flat files (DTT) 806
fluidics protocol
bypassing steps 112
editing 113
resuming 111
running 110
setting up 109–110
GCOS server tasks
cancel or restart 376
GCOS Services 56
Configuring 587
requirements for using 587
Start/Stop Service policies
601, 612
fluidics station
configuring 74
editing ID 115
priming 106–109
four-color arrays 130
GCOS Transfer Service 599
gene information database 47
GeneChip assay
overview 38–47
G
Gamma 678
GCOS
installing
new users 9–15
installing library files (new
install) 19–25
installing library files (upgraded install) 25–32
starting 53
troubleshooting 716
user interface 61–67
GCOS Administrator
Space Manager 464
starting 455
GCOS Analysis Service 598
GCOS Manager
functions 350
Import tab 396
Process tab 356
GeneChip AutoLoader 731
graphs
intensity bar graph 279
scatter graph 260–274
series graph 274, 279
grid 333
aligning 154
aligning main grid 154
aligning subgrid 162
viewing 151
grid alignment 147
H
highlights 202, 331
hybridization 43
873
I
image data
calculating average intensity
205
image settings 196–204
probe cell intensity
cell image view 205
measured image view
205
image data file 773, 782
image settings 196–204, 328–
333
cell coordinates 329
color 329
current image only 197
global 198
grid 333
highlights 202, 331
intensity 328
intensity range 199
pixel coordinates 200, 329
Image window 141
opening multiple windows
143
task bar 146
import tab
filter samples 397
windowpanes 396–400
importing data 400–414
associate data and samples
408–413
remove a sample for import
407
specify sample for import
402–408
start import 414
importing files
Batch Analysis Window 310
inc ratio
empirical analysis 641
inc/dec
empirical analysis 642
874
installing
GCOS
new users 9–15
library files (new GCOS install) 19–25
library files (upgraded GCOS
install) 25–32
instrument installation 541
intensity 328
intensity bar graph 279–283
clearing 283
options 280
plotting 280
intensity range 199
Internet Browser window 266
invalid character
in XML file used with Data
Transfer Tool 863
invalid characters 863
IUPAC base codes 691
J
Affymetrix® GeneChip® Operating Software User’s Guide
mask file 659
masks
See probe mask.
measured images
expression probe array 257
metrics
empirical algorithm 638
statistical expression algorithm 636
metrics table 245, 246
exporting 246–249
MIAME sample template 427
Microsoft SQL Server database
47, 389
MSDE database 47, 389
neg change
empirical analysis 642
NetAffx 252
normalization 655–665
all probe sets 657
selected probe sets 658
user defined 656
normalization mask file
creating 659
editing 663
selecting 661
L
library files 685
new GCOS install 19–25
upgraded GCOS install 25–
32
license
troubleshooting 720
log avg
online documentation 5
Oracle database 47
Oracle publish database 393
outliers
masking 216
unmasking 217
viewing 215
empirical analysis 639
empirical analysis 642
aligning 154
display options 250
exporting 252
pixel coordinates 200, 329
pos change
empirical analysis 642
pos fraction
empirical analysis 639
pos/neg
empirical analysis 640
cell intensity data 341
image data 341
report 343
privilege settings
functions defined 447
probe array
highlighting tiles 211
hybridization 43
notation 627
scanning 43, 751–786
tiling information 208
probe array type
delete 366, 385
cell image view 205
measured image view 205
probe cells
calculating average intensity
205
data 205–207
viewing data 209
probe mask 665–674
creating 666
editing 671
selecting 669
P
main grid
change 461
perturbation 678
pivot table 249
probe cell intensity
O
log avg ratio change
M
empirical analysis 639
password
printing
N
JPG files
created during DAT file archiving 217
viewing 217
pairs in avg
pair used
empirical analysis 639
Index
probe set
descriptions 251
obtaining information 252
probe set information
finding 253
hiding 256
reordering or removing 255
sorting 254
process data
delete 364
R
automatic backup 462
find feature 376–380
process tab
GCOS server 369
register GCOS server 460
renaming 67
experiment, sample, project
67
renaming feature 67
report
printing 343
reports
expression analysis 283–289
roles
filter samples 380
functions 358
windowpanes 356–358
create 444–448
define privileges 446–448
delete 451
delete a user 450
naming 444
role membership 448
project 67
renaming 67
publish database 47
accessing 384
capacity 389
create 388–396
Oracle on GCOS server
393
SQL on GCOS server
391
workstation 389
locations and sizes 389
selecting 316
publish tab windowpanes 381–
383
published data
delete 386
publishing 46
canceling a task 322
intensity data 320
overwriting data 321
publishing a task 321
restarting a task 322
specifying a task 316
scanner
register
process database 47
875
roles tab windowpanes 443–
444
S
sample
registering 41, 80
renaming 67
sample history
data view 91
displaying 91
process view 91, 93–95
scale factor 646
scale factor mask file
creating 649
editing 653
selecting 651
scaling 645–655
all probe sets 646
selected probe sets 648
user defined 646
configuring 75
GeneChip Scanner 3000 561
CE Mark Declaration of
Conformity 583
laser safety 566
regulatory 584
scanning a probe array
121–130
shutdown 133
shutting down 133
specifications 577
stopping a scan 132
troubleshooting 577
scanning 43, 751–786
scatter graph
options 269
plotting 261
selecting points 267
series graph 274–279
options 277
plotting 275
shortcut bars 61–64
GeneChip Software 61
Instrument Control 63
Settings 64
Signal 628
signal calculation 632
signal log ratio 628, 635
high 629
low 628
single-array analysis 226–228,
630
single-array analysis results
statistical algorithm 636
sort score 644
sorting
probe set information 254
Space Manager 464
SQL server 2000 publish database 391
Start/Stop Service policies
for GCOS Services 601, 612
876
stat common pairs 628
stat pairs 628
statistical expression algorithm 287–289, 636
status log 67, 234
subgrid alignment 162
Affymetrix® GeneChip® Operating Software User’s Guide
transfer data
into GCOS 808
out of GCOS 837
Transfer Service 599
troubleshooting 715, 787
autoloader 787
GCOS 716
GCOS Manager 721
CustomSeq for Resequencing arrays 172
subgrids 148
U
T
unarchiving data 361
unregister GCOS server 460
user interface 61–67
userset
task bar 146
tau 678
technical support 6
template tab windowpanes
create 417–420
delete 424
modify 421–424
426–427
templates
activate attributes 440
attributes 439
create 428–437
deactivate attributes 440
deactivate or activate 438
edit 437
edit attributes 441
insert attributes 440
MIAME 427
rename 438
testing
DMT 518
GCOS Manager 471, 523
userset tab windowpanes 415–
417
W
windowpanes
resizing 705
windows
Expression Analysis window (EAW) 46, 242
GCOS Administrator 456
GCOS Manager 349
Image window 141
Internet Browser 266
workflow monitor 39, 95
tiles
highlighting 211
tiling information 208
toolbars
Batch Analysis Window 698
main 695
publish 699
report 698
TOUGH-SPOTS™ 122
Tough-Spots™ 763
cell intensity analysis tab
100
grid alignment tab 98
hybridization tab 98
probe array analysis 100
publish tab 100
scan tab 98
workstation database
property information 466
relocate 466
space information 466
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