SOFTMAX PRO Formula Guide

SOFTMAX PRO Formula Guide
FORMULA REFERENCE GUIDE
FOR SOFTMAX® PRO SOFTWARE
Molecular Devices Corporation
1311 Orleans Drive Sunnyvale, California 94089
Part #0112-0141 Rev. A
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
Molecular Devices Corporation
Formula Reference Guide for
SoftMax Pro Software
Copyright
© Copyright 2007, Molecular Devices Corporation. All rights reserved. No part of this publication
may be reproduced, transmitted, transcribed, stored in a retrieval system, or translated into any
language or computer language, in any form or by any means, electronic, mechanical, magnetic,
optical, chemical, manual, or otherwise, without the prior written permission of Molecular Devices
Corporation, 1311 Orleans Drive, Sunnyvale, California, 94089, United States of America.
Trademarks
SoftMax is a registered trademarks of Molecular Devices corporation. Other trademarks used in this
manual are the property of their respective owners.
Disclaimer
Molecular Devices Corporation reserves the right to change its products and services at any time to
incorporate technological developments. This manual is subject to change without notice. Although
this manual has been prepared with every precaution to ensure accuracy, Molecular Devices
Corporation assumes no liability for any errors or omissions, nor for any damages resulting from the
application or use of this information.
Questions?
Phone: +1-800-635-5577
+1-408-747-1700
Fax: +1-408-747-3603
Web: www.moleculardevices.com
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Contents
1. Introduction
Formula Categories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Reduction Formulas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Column Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Summary Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Formula Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Formula Building Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Lists of Numbers and Arrays of Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Formula Naming Conventions in SoftMax Pro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Referencing Objects in Different Sections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Ordering Functions in Complex Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Rules to Follow When Writing Formulas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Special Characters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Referencing Columns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Evaluating Column Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Strings in Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2. Operators
Mathematical Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Using Mathematical Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Comparison (Logical) Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Conditional (Boolean) Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Using Comparison and Conditional Operators . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Concatenation Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Concatenating Text Strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Concatenating Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
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Contents
3. Functions
Mathematical Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Statistical Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Interpolation Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
VMax Reduction Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Other Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
NANs/MakeErrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Text Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4. Accessors
Plate/CuvetteSet Setup Information Accessors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Kinetic and Spectrum Data Accessors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Plate Data Accessors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
PathCheck Accessors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Group and Well Information Accessors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Blank Accessors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
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1. Introduction
The Formula Reference Guide for SoftMax Pro software identifies and enumerates all the
details about formulas, accessors, and functions that you can use to create powerful data
analysis templates, that when saved as Protocol files, can completely automate the analysis
and results reporting for all your microplate reads.
Chapter 1 provides a general introduction to SoftMax Pro formulas, while Chapters 2
through 4 list the building blocks used in SoftMax Pro formulas and give brief examples
of how to use them.
This Formula Reference Guide assumes that the user understands the basics of SoftMax
Pro software. For more information on using the software, please review the SoftMax Pro
User Guide.
1.1.
FORMULA CATEGORIES
Formulas are broken down into categories:
1.1.1.
>
Reduction formulas are used in Plate and CuvetteSet sections and apply a formula to
an entire Plate section or CuvetteSet section.
>
Column formulas are used in Group sections and apply a formula to a single column in
the Group section.
>
Summary formulas may be used in either Group or Notes sections and are generally
used to reduce data to a single value or array.
REDUCTION FORMULAS
Reduction formulas can be used in Plate and CuvetteSet sections. Reduction formulas
apply only to the specific Plate or CuvetteSet section for which they are written and the
formulas determine the values that are reported in the Values column of the Group section(s). Unlike formulas in Group sections and Summaries, Reduction formulas must
evaluate to a number (not text). Up to two types of formulas (that work in conjunction
with each other) can be used to reduce plate and/or cuvette data, depending on the instrument and read mode you are using.
Wavelength Combination: This formula modifies raw data. It is available for all read
modes with all instruments and is the only reduction available for Endpoint or Dual Read
(not available on all instruments; please see your specific instrument manual for more
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1. Introduction
information). These formulas act on all data from each well or cuvette in the
Plate/CuvetteSet sections.
Kinetic, Spectrum, or Well Scan Reduction: These formulas use the data values after the
Wavelength Combination and produce a single, reduced value for each well or cuvette.
If default reductions do not meet your needs, custom formulas can be created. To enter a
custom formula:
1 Click the Reduction button or select Plate > Reduction.
2 Select Custom from one of the drop-down lists (the choices that are available in the
Reduction dialog box will depend on the read mode and instrument type).
3 Click the =ƒ[x] button to open a Calculation dialog box. This dialog box has only one
field in which to create or edit a formula.
4 Enter the formula into the field and click OK.
5 Click OK in the Reduction dialog box to close that dialog box and set the parameters.
For example, you can multiply the raw data by a constant such as:
!Lm1*1.2
or with two-wavelength reads, a ratio analysis might be desired:
(!Lm1 - !Lm2)/!Lm2
where Lm1 and Lm2 represent raw data (OD, RFU, RLU) for the two wavelengths
respectively.
1.1.2.
COLUMN FORMULAS
Column formulas act on either raw or reduced numbers from Plate/CuvetteSet sections
and evaluate to a list of numbers or text. Column formulas are used in Group sections and
contain a name that is used as the column’s header (i.e., its name in the Group section)
and a formula. Column formulas can be referenced by name in other formulas.
Group sections sort information by the sample names assigned in the Template Editor.
Data comes into the Group section in “template order” (the order assigned in the template) rather than in “well order” (the order in which it was acquired from the instrument). For example, if wells A1, A2, B1, B2, C1, and C2 are assigned to a single group
named Samples, data from those wells is displayed in a Group section named Samples and
is sorted by sample name. The numbers in the Values column of the Group section are
dictated by the Reduction formula in the Plate section. The formula for the Values column is “!Wellvalues”.
Note: “Values” is the default name, but it can easily be changed.
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1.2. Formula Size
When writing custom formulas to access raw data in the Plate section, it is necessary to
include “well” so that the values are sorted by template order. Examples include
!WellLm1, !WellLm2 and !WellPathlength.
Column formulas evaluate an entire column on a row-by-row basis. When writing column formulas to access data from two or more Group sections, the Group sections must
have the same number of rows in them. If Group section A has 3 rows and Group section
B has 4 rows, a formula in Group section B that refers to a column in Group section A is
only evaluated for the first 3 rows because only 3 row-by-row comparisons can be made.
There are occasions when one does not want the data in a column of a Group section
sorted by template order. In the case of a Spectrum scan, one might want the wavelength
values in one column and OD values for a single well in another. The corresponding formulas for well B1 in Plate#X would be [email protected]#X and [email protected]#X.
1.1.3.
SUMMARY FORMULAS
Summaries consist of four parts:
>
A Summary name (which is used to refer to the Summary in other formulas).
>
A description (optional).
>
The formula itself.
>
A specification for the number of decimal places to which the formula results should be
displayed.
Summaries can be used in Group sections and Notes sections, and evaluate to either a single number or a list of numbers. Summaries report information from Plate, CuvetteSet,
Graph, or Group sections, or to a combination of these.
Summaries can be edited by double-clicking them or by highlighting them and then clicking the =ƒ(x) button in the tool bar (both actions open the Calculation dialog box).
1.2.
FORMULA SIZE
Formula length in SoftMax Pro is limited to 255 characters. This limitation can be an
issue when creating complex formulas or if object names are long.
It is generally recommended to break up complex formulas into several simpler formulas,
and to use short object names (Experiment name, Section names, Group names, etc.).
To do this, you can create two or three columns (or a combination of columns and Summaries), each containing a portion of the calculation, rather than one column with an
extremely complex formula (to simplify the view of the Group section, you can hide the
columns containing intermediate steps).
Alternatively, you can use Summaries to contain intermediate steps. If the 255-character
limit becomes a problem and you cannot break the formula up into several smaller formulas, you can also shorten all of the object names.
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1. Introduction
1.3.
FORMULA BUILDING BLOCKS
SoftMax Pro uses four types of formula building blocks:
>
Operators allow you to combine other building blocks together. Operators are discussed in Chapter 2.
>
Functions are mathematical or text items that perform operations within SoftMax Pro
(for example, standard deviation or slope). Functions are discussed in Chapter 3.
>
NANs (Not A Number) are text items that are considered to be numbers by SoftMax
Pro. NANs are discussed in Chapter 3.
>
Accessors allow you to access data and other information from objects (Plates, CuvetteSets, etc.) and functions (VMax Rate, the wavelength at which a Spectrum scan was
begun, etc.). Accessors are unique to SoftMax Pro and are discussed in Chapter 4.
Some formula building blocks can be used alone. Others must always be used in conjunction with other building blocks. A complete listing of these building blocks, along with
examples showing how to use them, is provided in Chapters 2 through 4.
1.4.
LISTS OF NUMBERS AND ARRAYS OF NUMBERS
SoftMax Pro can perform calculations on lists of numbers and arrays (lists of lists) of
numbers. An example of a list of numbers is a single column in a Group section or a single
set of Endpoint values. The column is also a 1 × N array, where N is the number of rows
in the column or values in the set of endpoints.
An example of an array of numbers is a column containing the optical densities at each
time point in a Kinetic run: it is a Y × X array, where Y is the number of ODs in each row
and X is the number of samples in the group that was assayed (and is also the number of
rows in the Group section).
1.5.
FORMULA NAMING CONVENTIONS IN SOFTMAX PRO
SoftMax Pro uses a hierarchical naming structure, much like the directories and subdirectories used in computer file systems. All objects (e.g., columns, Summaries, wells, graphs,
plots) in SoftMax Pro have names and, when writing formulas, the names are used to refer
to the objects.
An object’s full name consists of the name of the object plus the name of the section the
object is in plus the name of the experiment in which the section is located. SoftMax Pro
uses the @ symbol to combine these references:
[email protected]@ExperimentName
[email protected]@ExperimentName
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1.6. Ordering Functions in Complex Formulas
Thus columns in two different Group sections can have the same name, but SoftMax Pro
differentiates between them because their full names are different:
[email protected]@Experiment1
[email protected]@Experiment1
[email protected]@Experiment2
1.5.1.
REFERENCING OBJECTS IN DIFFERENT SECTIONS
If a formula refers to an object that is in the same section as the formula, the object’s section and experiment names are not required.
If the object is not in the same section as the formula and you do not reference the object’s
section and/or experiment name, SoftMax Pro uses the first object of that name that it
finds in the file.
For example, suppose Group sections 1 and 2 both contain a column called Values, Group
section 3 does not contain a column of that name, and you are writing a formula in
Group section 3 that subtracts Group section 2’s Values column from a column named
“ColX” in Group section 3.
If you write:
ColX - Values
SoftMax Pro finds the first occurrence of an object named “Values” in the file and fills in:
ColX - [email protected]
That is, it subtracts the Values column from Group section 1 from ColX.
To write the formula to give the desired result, you must specify the section in which the
desired Values column is found:
ColX - [email protected]
1.6.
ORDERING FUNCTIONS IN COMPLEX FORMULAS
Formulas can be very simple. For example, Average(Values) takes the average of a Group
section column named Values and returns a single value. Formulas may also be quite complex, combining several functions or accessors together. These more complicated formulas
are called nested formulas because parentheses are used to ‘nest’ different functions within
one another.
The order in which the functions are nested determines the order in which they will be
processed. SoftMax Pro processes the information contained within parentheses before the
information outside the parentheses. If multiple sets of parentheses are present, informa-
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1. Introduction
tion is processed from inside to outside, starting with the innermost set of parentheses. An
example of a simple nested formula is:
Sqrt(Average(Values))
This formula first calculates the average of the column named “Values” then takes the
square root of that average.
1.7.
RULES TO FOLLOW WHEN WRITING FORMULAS
1.7.1.
CASE
SoftMax Pro formulas are not case sensitive: “Average”, “average”, and “AVERAGE” are
treated the same and return the same values.
1.7.2.
SPECIAL CHARACTERS
If an object’s name contains a space, starts with a number, or includes any of the following
special characters: # $ % / * ?, the name must be enclosed in single quotation marks. For
example, ‘OD Values’.
Do not use ^ @ ~ or & in object names because these characters have special meanings in
SoftMax Pro. Using these characters in formulas can cause errors when the objects are
referred to in other formulas.
1.7.3.
REFERENCING COLUMNS
When writing a formula that references columns in more than one Group section, make
sure the Group sections all have the same number of rows (samples).
For example, if one Group section has 10 rows and another has 12 rows, and a formula is
multiplying values from each Group section row by row, the output is undefined for rows
11 and 12.
1.7.4.
EVALUATING COLUMN FORMULAS
Column formulas must evaluate either to text, to numbers, or to a Boolean (i.e., to True
or False) because SoftMax Pro does not allow a column to contain both text (“Pass”) and
numeric (“1.002”) results.
However, you can use NANs to put text into a column of numbers (because SoftMax Pro
treats NANs as numbers) or you can report numbers as text strings.
1.7.5.
STRINGS IN FORMULAS
When a formula includes a result that the user wants displayed, these text results must be
enclosed in double quotation marks (“ “), for example: “Out of Range”.
Wavelength reduction formulas in Plate or CuvetteSet sections must evaluate to numbers
(however, NANs are considered numbers and can be used to bypass this restriction).
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2. Operators
Chapter 2 describes the different types of operators that can be used to build formulas in
SoftMax Pro. Operators allow you to combine and compare numbers, functions, accessors, and text strings in a variety of ways within formulas.
Recall that formulas beginning with !Lm1, !Lm2, etc., are suitable for Reduction formulas
in Plate/CuvetteSet sections. In Group sections, the analogous formulas must begin with
!WellLm1, !WellLm2, etc., to ensure sorting according to the Template. To access data
from single wells, the accessors are !a1Lm1, !a2Lm1,etc., (in Reduction formulas) and
[email protected]#X, [email protected]#X.,etc., (in Column or Summary formulas).
2.1.
MATHEMATICAL OPERATORS
The list below reports the mathematical operators that can be used in SoftMax Pro formulas and describes their function, with which types of data they can be used, and gives
examples of how to use them.
SoftMax Pro uses the standard mathematical order for operators: multiplication and division are performed before addition and subtraction (regardless of their order in the equation) unless you use parentheses to order the operations.
Mathematical
Description
Operator
*
Multiplication: Returns the product of 2 numbers, 2 lists of numbers, or
2 arrays of numbers. You can also multiply a list or array of numbers by
a constant.
!Lm1 * 10
(Reduction formula)
/
Division: Returns the quotient of 2 numbers, 2 lists of numbers, or 2
arrays of numbers. You can also divide a list or array of numbers by a
constant.
!WellLm1 / !WellLm2
(Group section formula)
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2. Operators
Mathematical
Description
Operator
+
Addition: Returns the sum of 2 numbers, 2 lists of numbers, or 2 arrays
of numbers. You can also add a constant to a list or array of numbers.
!WellLm1 + !WellLm2
-
Subtraction: Returns the difference between 2 numbers, 2 lists of
numbers, or 2 arrays of numbers. You can also subtract a constant
from a list or array of numbers.
!Lm1 - !A12Lm1
(Reduction formula)
^
Exponent: Raises a number to another power. You can take the
exponent of individual numbers, lists of numbers, or arrays of
numbers.
!WellLm1 ^ 2
Mod
Remainder: Returns the remainder from dividing 2 numbers. You may
take the remainder for individual numbers, a list of numbers, or an
array of numbers.
11 mod 3
()
Parentheses: Used to order multiple mathematical operations;
operations in inner parentheses are performed first.
(!Lm1 + !A12Lm1) * !H1Lm1
2.1.1.
USING MATHEMATICAL OPERATORS
The following two examples show different ways in which you can use mathematical
operators. The first example shows how to multiply two lists of numbers in a Group section; the second shows how to multiply optical densities in a Plate section by a constant.
Example: Multiplying Lists of Numbers
When multiplying lists of numbers in SoftMax Pro you can refer to them by name, or use
functions (see Chapter 3, “Functions”) or accessors (see Chapter 4, “Accessors”) to refer to
them. For example, suppose you have a column named “AdjResults” that contains the
average of the result for each sample multiplied by the dilution factor, generated by the
formula “MeanResult * Factor”. MeanResult is another column that is itself generated by
the formula “Average(Results)”.
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2.2. Comparison (Logical) Operators
The formula for AdjResults can be written in any of the following ways:
MeanResult*Factor
MeanResult*Dilution
MeanResult*!SampleDescriptor
Average(Results)*!SampleDescriptor
Average(Results)*Dilution
Example: Multiplying Optical Densities by a Constant
DNA samples were read in a SpectraMax at 260 nm with PathCheck selected. The optical
density values were multiplied in the Group section by a constant to report the concentration of DNA in each well.
The formula for the reduced number is:
!WellLm1*50
2.2.
COMPARISON (LOGICAL) OPERATORS
Comparison operators are used to compare numbers, lists of numbers, arrays of numbers,
or text strings. They are used most frequently in conditional statements (see Section 2.3.,
“Conditional (Boolean) Operators”). When used by themselves, comparison operators
return “True” if the argument is true, and “False” if the argument is false.
Comparison
Description
Operator
=
Equals: Determines if two numbers, lists of numbers, or arrays of
numbers are equal to one another.
!Lm1 = !Lm1 is True
!Lm1 = !A12Lm1 is False
>
Greater Than: Determines if a number, list of numbers, or array of
numbers is greater than another number, list of numbers, or array of
numbers.
(2*!Lm1) > !Lm1 is True
!Lm1 > !Lm1 is False
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2. Operators
Comparison
Description
Operator
>=
Greater Than or Equals: Determines if a number, list of numbers, or
array of numbers is greater than or equal to another number, list of
numbers or array of numbers.
Lm1 >= !Lm1 is True
(2*!Lm1) >= !Lm1 is True
!Lm1 >= (2*!Lm1) is False
<
Less Than: Determines if a number, list of numbers or array of numbers
is less than another number, list of numbers or array of numbers.
Lm1 < (2*!Lm1) is True
(2*!Lm1) < !Lm1 is False
<=
Less Than or Equals: Determines if a number, list of numbers, or array of
numbers is less than or equal to another number, list of numbers, or
array of numbers.
!Lm1 <= !Lm1 is True
(2*!Lm1) <= !Lm1 is False
!Lm1 <= (2*!Lm1) is True
<>
Does Not Equal: Determines if two numbers, lists of numbers, or arrays
of numbers are not equal to one another.
!Lm1 <> !Lm1 is False
(2*!Lm1) <> !Lm1 is True
Example: Reporting Whether Data Reaches a Threshold Value
Create a column with the formula:
MeanValue > 0.2
This comparison formula evaluates to True if an optical density (i.e., the MeanValue) is
greater than 0.2 and False if it is not.
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2.3. Conditional (Boolean) Operators
2.3.
CONDITIONAL (BOOLEAN) OPERATORS
Conditional operators allow you to compare results in Plate/CuvetteSet sections, Group
sections, and Summaries. They can be used to set criteria for evaluating numerical results.
Group sections and Summaries can evaluate either to a number or to text, whereas Plate/
CuvetteSet sections can evaluate only to a number.
For example, an ELISA kit may ask you to determine whether a sample is positive, negative, or requires retesting based on the values of the assay controls.
Conditional
Description
Operator
If
Compares numbers, lists of numbers, or arrays of numbers to each
other.
If (Condition, Value-If-True, Value-If-False)
If (!WellLm1 > [email protected]#X,
“Above threshold”, “Below threshold”)
For this example: If the value at wavelength 1 in a well is greater than the
value in well A12 of Plate#X, return “Above threshold”, otherwise return
“Below threshold”.
And
Compares numbers, lists of numbers, or arrays of numbers.
Returns True if all of the arguments are true.
Returns False if any of the arguments are not true.
WellLm1 > [email protected]#X And
!WellLm2 > [email protected]#X
Or
Compares numbers, lists of numbers, or arrays of numbers.
Returns True if any of the arguments are true.
Returns False only if all of the arguments are false.
WellLm1 > [email protected]#X Or
!WellLm2 > [email protected]#X
Not
Reverses the logic of an argument.
If something is not true, it is false; if it is not false, it is true.
Not(!WellLm1 > [email protected]#X And !WellLm2 >
[email protected]#X)
False
Returns the logical value False.
True
Returns the logical value True.
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11
2. Operators
2.3.1.
USING COMPARISON AND CONDITIONAL OPERATORS
Conditional formulas use Boolean logic, which treats various classes of data as algebraic
quantities. The use of both Boolean (conditional) and logical (comparison) operators in
formulas allows you to combine several simple mathematical operations into a single,
more complex operation or function. SoftMax Pro also allows you to nest (embed) conditional statements within other conditional statements, allowing multiple conditions and
outcomes in a single formula.
Simple Conditional Formulas
Conditional formulas have the general form:
If (Condition, Value-If-True, Value-If-False)
The table below shows several examples of relatively simple conditional formulas.
Condition
Conditional Formula
Value-If-True
Value-If-False
If (!WellLm1 > 0.5, ”Pass”, ”Fail”)
!WellLm1 > 0.5
”Pass”
”Fail”
If (!WellLm1 > 0.5 And !WellLm2 > 0.4,
”Pass”, “Fail”)
!WellLm1 > 0.5 And !WellLm2 > 0.4
”Pass”
”Fail”
If (MeanValue > Summary#[email protected]
MeanValue > Summary#[email protected] and
and MeanValue < Summary#[email protected],
MeanValue < Summary#[email protected]
“Acceptable”, “Out of Specification”)
“Acceptable”
“Out of Specification”
Nested Conditionals
Conditional statements can also be written to have multiple conditions and multiple outcomes. A conditional statement always has one outcome more than the number of conditions.
For example, a conditional statement with two conditions has three outcomes:
If (Condition#1,Outcome if Condition#1 is True, (if(Condition#2, Outcome if
Condition#2 is True, Outcome if Condition#2 is False))
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2.3. Conditional (Boolean) Operators
In this formula, if Condition#1 is true, an outcome is returned, but if Condition#1 is
false, Condition#2 is evaluated. If Condition#2 is true, a second outcome is returned; if it
is false, a third outcome is returned.
You can create very complicated formulas by nesting multiple conditional statements,
with the following constraints:
>
The entire formula must not exceed 255 characters.
>
The formula must specify an outcome if true and an outcome if false for each condition.
>
The formula must state a condition, the outcome if true; then a new nested condition
if the previous condition was false and the outcome if the second condition is true; and
so on until the last condition, with final outcomes for if the last condition is true or
false.
The general format is:
If(Condition#1, outcome when Condition#1 is True, (if(Condition#2, outcome
when Condition#2 is True,(if(Condition#3, outcome if Condition#3 is True...(if
Condition#X, outcome if Condition#X is True, outcome if Condition#X is
False)))))...).
An outcome in this type of conditional statement can be conditional, with its own True/
False outcome embedded in the Value-If-True outcome of the first condition.
An example of this type of complex, nested conditional statement is given below. The formula has been written to include several samples with 5 different controls. The information for the different controls is provided by Summary formulas named LL, LH, LM, MH
and HH, respectively, and the Summary formulas are located in a Notes section named C.
Formula
If( Sample#=1,
If( Values>[email protected] and Values<[email protected], “Blue”, “Yellow”),
If( Sample#=2,
If( Values>[email protected], “Red”, “Green”),
If( Sample#=3,
If( Values>[email protected] and Values<[email protected],
“Orange”, “Purple” ),
”White“ )
)
)
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13
2. Operators
Diagram
Example: A Conditional Formula with One Condition and Two Outcomes
Below is an example of a simple conditional statement, written as a Summary formula for
a Group section. This conditional statement has one condition with two outcomes:
>
If the minimum number in a column named Values is greater than 2, the formula
reports “Acceptable”.
>
If the minimum number is equal to or less than 2, the formula reports “Out of Specification”.
Formula
If(Min(Values)>2,“Acceptable”,“Out Of Specification”)
Breakdown
Condition: Min(Values)>2
Value-If-True:“Acceptable”
Value-If-False:“Out of Specification”
If the Group section does not have any data, the formula evaluates to the default (False
condition) and reports “Out of Specification”.
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2.3. Conditional (Boolean) Operators
Example: A Conditional Statement with Two Conditions and Three Possible Outcomes
Below is an example of a wavelength combination formula that has 2 conditions and 3
outcomes:
>
The first condition stipulates if the values for Lm1 in all wells are less than the value of
Lm1 in well A12, report the NAN MakeErr(118) (which displays the word “Low”); if
they are equal to or greater than the value in well A12, apply the second condition.
>
The second condition stipulates if the values for Lm1 in all wells are greater than the
value of Lm1 in well H1, report NAN MakeErr(117) (which displays the word
“High”); otherwise, if this condition is not true, report NAN MakeErr(123) (which
displays “*****”).
NANs, including MakeErr functions, are discussed in detail in Chapter 3, “Functions”.
Formula
If(!WellLm1<[email protected]#X, MakeErr(118), (If(!WellLm1>[email protected]#X,
MakeErr(117), MakeErr(123))))
Breakdown
Condition#1: !WellLm1<[email protected]#X
Value-if-Condition#1 True: MakeErr(118) (= “Low”)
Condition#2: !WellLm1>[email protected]#X
Value-if-Condition#2 True: MakeErr(117) (= “High”)
Value-if-Condition#2 False: MakeErr(123) (= “*****”)
Tips for Writing Conditional Formulas
1 When writing a complex or nested conditional statement, it is best to break it into
several simple or smaller conditional statements and then combine them.
2 Nesting conditional statements requires multiple pairs of parentheses. Make sure that
you have the same number of opening and closing parentheses.
3 In general, one more outcome than the number of conditions is always present (i.e., 1
condition with 2 outcomes, or 2 conditions with 3 outcomes, etc.).
4 Outcomes must evaluate to all numbers or all text.
For example, if the True outcome of a formula evaluates to a number, the False
outcome of the same formula must evaluate to a number and cannot evaluate to text.
However, if a conditional statement evaluates to numbers, you can use SoftMax Pro’s
predefined NANs to include text in the results (see Section 3.6., “NANs/MakeErrs”).
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15
2. Operators
Likewise, if a conditional statement evaluates to text, you can return numbers as a
result as long as the numbers are treated as text (see Section 3.7., “Text Functions”).
5 When no data is present in a file (i.e., data has not been collected yet), conditional
formulas default to return the False outcome. Therefore, conditional formulas should
be written such that the last outcome is the outcome you want to see as the default.
For example, if a conditional formula reports “Pass” or “Fail”, you should write the
formula so that it defaults to reporting “Fail” so it does not return a positive result
when the file does not contain data.
For example, both sample formulas below report “Pass” if the Values are less than or
equal to 0.2 and report “Fail” if they are greater than 0.2.
If(Values > 0.2, ”Fail”, ”Pass”)
If(Values <= 0.2, ”Pass”, ”Fail”)
Because the first formula is written such that “Pass” is the False outcome, the default
result when no data is present is “Pass.” The second formula is a better way to write this
conditional because “Fail” is the False outcome and is reported as the default result
when no data has been collected.
2.4.
CONCATENATION OPERATORS
In SoftMax Pro, two operators concatenate lists of numbers and arrays of numbers, and a
third operator concatenates text strings. These operators allow you to perform complex
data analyses using relatively simple formulas.
2.4.1.
CONCATENATING TEXT STRINGS
Operator
+
Description
Combines two text strings.
“SOFT”+ “Max” = “SoftMax”
2.4.2.
CONCATENATING NUMBERS
Operator
& (ampersand)
Description
Combines several lists of numbers into a single list of numbers.
X&Y&Z
~ (tilde)
Combines several lists of numbers into an array of numbers.
X~Y~Z
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2.4. Concatenation Operators
The difference between ~ and & is illustrated briefly below and is then followed by examples from SoftMax Pro.
List A
List B
1
5
2
6
3
7
4
8
A&B
A~B
1
1
5
2
2
6
3
3
7
4
4
8
5
6
7
8
Example: Using & in a Column Formula
Suppose we have a Plate section that collected Kinetic data at four wavelengths and Lm2
and Lm4 are identical. !WellLm2 and !WellLm4 are the optical densities collected at each
time point in each well at the second and fourth wavelengths, reported into the Group
section in template (or group) order.
The & operator can be used to combine !WellLm2 and !WellLm4 into a single list of
numbers, which can then be used to determine the maximum value of the list:
Max(!WellLm2 & !WellLm4)
This formula returns the maximum value of the item within the parentheses.
Example: Using ~ in a Group section (1)
Suppose we have four columns AvgOD490, AvgOD590, AvgOD620 and AvgOD670
that report the average optical density value of several wells at the specified wavelengths
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17
2. Operators
from a Spectrum scan. We can define a new column MaxOD to report the maximum OD
from each of the columns using the ~ function:
Max(AvgOD490 ~ AvgOD590 ~ AvgOD620 ~ AvgOD670)
Example: Using ~ in a Group section (2)
We can use the tilde operator to bring information into a Group section directly from the
wells of the plate, bypassing the group structure setup in the template (i.e., the data are
entered in well order, not group order). Consider the following formula:
Average([email protected]#1 ~ [email protected]#1 ~ [email protected]#1 ~ [email protected]#1 ~
[email protected]#1 ~ [email protected]#1 ~ [email protected]#1 ~ [email protected]#1)
The information from the Spectrum scans in these wells is averaged together on a wavelength-by-wavelength basis and is reported in a column (i.e., the data obtained from wells
A12, B12, C12, D12, E12, F12, G12, and H12 at 190 nm are averaged, the data
obtained from wells A12, B12, C12, D12, E12, F12, G12, and H12 at 191 nm are averaged, etc.).
Formulas such as this one are very powerful because they enable you to bring Spectrum
scan or Kinetic run information into a Group section and perform complex analyses such
as averaging wells on a point-by-point basis, graphing the wells (or groups of wells) in the
Graph section and applying different curve fits, or subtracting two Spectrum scans on a
point-by-point basis and then plotting the difference.
Formulas that bring information into the Group section directly from the Plate section,
bypassing the template, should be used with caution because the information in the
Group section does not correspond to the well assignments in the template.
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3. Functions
The general format for the many SoftMax Pro built-in functions is:
FunctionName(Parameter1, Parameter2, Parameter3)
Functions can have zero to three parameters input to them. Lists of numbers, arrays of
numbers, and lists of text strings can be used as input parameters, and the function can
return either lists or arrays of numbers or text as appropriate. Functions return numbers,
text, or Booleans.
If a function has more than one parameter, the order in which the parameters are listed is
extremely important. If the parameters are entered in the incorrect order, the function will
return erroneous results.
SoftMax Pro functions are divided into the following categories:
3.1.
>
Mathematical functions
>
Statistical functions
>
Reduction functions
>
Interpolation functions
>
Other functions
>
NANs
>
Text functions.
MATHEMATICAL FUNCTIONS
Mathematical functions take numbers, lists of numbers, or arrays of numbers as parameters and return corresponding numbers, lists of numbers, or arrays of numbers. For example, if a list of numbers is given as the parameter, a list of numbers is returned as the result.
The mathematical functions in SoftMax Pro are all common mathematical, algebraic, and
trigonometric functions, and can be used alone or in combination with other functions,
accessors, or operators to create more complex formulas.
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19
3. Functions
Trigonometric functions are calculated in radians (180 degrees = pi radians).
Function
Abs(Parameter)
Description
Returns the absolute value of a number, list of numbers, or array of
numbers.
Abs(-10) = 10
Acos(Parameter)
Returns the arccosine of a number, list of numbers, or array of
numbers.
Acos(-0.25) = 1.82348
Acos(!CombinedPlot)
Asin(Parameter)
Returns the arcsine of a number, list of numbers, or array of
numbers.
Asin(-0.25) = 0.25268
Asin(ColumnX)
AntiLog(Parameter)
Returns the antilog (base e) of a number, list of numbers, or array
of numbers. It is equivalent to e^(X) where X is a number, list of
numbers, or array of numbers.
Antilog(1) = 2.718
Antilog(Summary#1)
AntiLog10
Returns the antilog (base 10) of a number, list of numbers, or array
(Parameter)
of numbers. It is equivalent to 10^(X) where X is a number, list of
numbers, or array of numbers.
Antilog10(1) = 10
Antilog(Results)
Atan(Parameter)
Returns the arctangent of a number, list of numbers, or array of
numbers.
Atan(0.25) = 0.24498
Atan(!Lm1)
Atan2(Parameter,
Returns the arctangent from X- and Y- coordinates. Both
Parameter)
parameters can be numbers, lists of numbers or arrays of
numbers. Both parameters should be of the same type, and have
the same number of items in them. Returns a single number, list of
numbers, or array of numbers from the two parameters entered.
Atan2(1, 1) = 0.78540
Atan2(Values, Concentration)
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3.1. Mathematical Functions
Function
Ceil(Parameter)
Description
Returns a number, list of numbers, or array of numbers rounded up
to the nearest integer.
Ceil(1.9) = 2
Ceil(-1.9) = -1
Ceil(Results)
Cos(Parameter)
Returns the cosine of a number, list of numbers, or array of
numbers.
Cos(0.25) = 0.96891
Cos(Values)
Cosh(Parameter)
Returns the hyperbolic cosine of a number, list of numbers, or
array of numbers.
Cosh(4) = 27.30823
Cosh(!WellLm1)
Exp(Parameter)
Returns e raised to the power of a number, list of numbers, or array
of numbers.
Exp(3) = 20.08554
Exp(Summary#3)
Fact(Parameter)
Returns the factorial of a number, list of numbers, or array of
numbers (a factorial is obtained by multiplying a series of
consecutive integers, beginning at 1 and ending at the specified
number, i.e., the factorial of 4 is 1 x 2 x 3 x 4).
Fact(4) = 24
Fact(Col#1)
Floor(Parameter)
Returns a number, list of numbers, or array of numbers rounded
down to the nearest integer. This function is the opposite of Ceil.
Floor(1.9) = 1
Floor(-1.9) =-2
Floor(Results)
Fract(Parameter)
Returns the fractional part of a number, list of numbers, or array of
numbers.
Fract(34.567) = 0.567
Fract(Values)
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3. Functions
Function
Int(Parameter)
Description
Returns the integer part of a number, list of numbers, or array of
numbers.
Int(6.9) = 6
Int(-6.9) = -6
Int(Results)
Ln(Parameter) or
Returns the natural logarithm of a number, list of numbers, or array
Log(Parameter)
of numbers.
Ln(5) = 1.60944
Ln(Values)
Log10(Parameter)
Returns the logarithm base 10 of a number, list of numbers, or
array of numbers.
Log10(5) = 0.69897
Log10(!Lm1)
Pi
Returns the value of pi (3.14159). No parameters.
Summary#1 * Pi
Rand
Returns a random number between 0 and 1. Takes no parameters.
Rand
Round(Parameter,
Rounds a number, list of numbers, or array of numbers to the
# of digits)
specified number of digits. The first parameter is a number, list of
numbers, or array of numbers. The second parameter is the
number of digits to the right of the decimal point the result will be
rounded to.
Round(3.456,2) = 3.46
Round(Results,2) rounds the values in a column named Results to
the hundredths.
Sign(Parameter)
Returns the sign of a number, list of numbers, or array of numbers.
If a number is positive, it returns 1; for a negative numbers it
returns –1; and for zero it returns 0.
Sign(25) = 1
Sign(-25) = -1
Sign (0) = 0
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3.1. Mathematical Functions
Function
Sin(Parameter)
Description
Returns the sine of a number, list of numbers, or array of numbers.
Sin(2) = 0.90930
Sin(Column1)
Sinh(Parameter)
Returns the hyperbolic sine of a number, list of numbers, or array
of numbers.
Sinh(1) = 1.17520
Sinh(Column1)
Sqrt(Parameter)
Returns the positive square root of a number, list of numbers, or
array of numbers.
Sqrt(64) = 8
Sqrt(Column1)
Tan(Parameter)
Returns the tangent of a number, list of numbers, or array of
numbers.
Tan(0.25) = 0.25534
Tan(ParmB)
Tanh(Parameter)
Returns the hyperbolic tangent of a number, list of numbers, or
array of numbers.
Tanh(-2) = -0.96403
Tanh(ParmB)
The functions above can be used singly as shown in the examples above, or they can be
used in combination with one another. For example:
Ceil(Abs(Values))
This formula takes the items in a column named Values, rounds them up to the nearest
integer and then takes the absolute value of that integer.
These functions can also be used in combination with other mathematical functions,
accessors, and operators to create more complex formulas.
If you use Round, Int, Ceil, and Floor when SoftMax Pro is set to display results to a set
number of decimal places, and if the number of decimal places specified for SoftMax Pro
is larger than the number specified for the individual function, the extra decimal places
are filled with zeroes. For example, if SoftMax Pro is set to display 3 decimal places and
you are rounding a number to two decimal places, the number is displayed as X.YZ0.
Similarly, integers are displayed as X.000.
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3. Functions
3.2.
STATISTICAL FUNCTIONS
Statistical functions behave differently depending on whether they are in a Summary formula or a Column formula:
>
Summary formulas: take a list of numbers as a parameter and return a single number.
>
Column formulas: take a 1-dimensional list of numbers (row or column) as a parameter and return a single number. If the column is a 2-dimensional array, a list of numbers
is returned, 1 value per row.
Statistical Function
Description
Average(Parameter)
Returns the average of a list or array of numbers.
AvgDev(Parameter)
Returns the average of the absolute deviation from the mean
of a list or array of numbers.
Cv(Parameter)
Returns the coefficient of variation of a list or array of
numbers.
Cvp(Parameter)
Returns the coefficient of variation (population) of a list or
array of numbers.
Max(Parameter)
Returns the maximum value in a list or array of numbers.
MaxDev(Parameter)
Returns the absolute value of the maximum absolute
deviation from the mean of a list or array of numbers.
Median(Parameter)
Returns the middle of list of numbers or array of numbers
after the list is sorted.
Min(Parameter)
Returns the minimum value in a list or array of numbers.
StDev(Parameter)
Returns the standard deviation of a list or array of numbers.
StDevp(Parameter)
Returns the standard deviation (population) of a list or array of
numbers.
StdErr(Parameter)
Returns the standard error of a list or array of numbers, which
is the standard deviation divided by the square root of the
number of values in the list or array.
Sum(Parameter)
Returns the sum of a list or array of numbers.
Example: Reducing an Array of Values to a Single Number per Well
Statistical functions are useful to reduce a list of values (e.g., Spectrum scan optical densities) to a single number per well.
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3.3. Interpolation Functions
For example, if you want the maximum values in a Spectrum scan, you would use the following formula:
Max(!Lm1) in the Plate section reduction or
Max(!WellLm1) in a Column formula.
Similarly, you can use Min(!Lm1) and Min(!WellLm1) to report the minimum optical
density. You can also combine these formulas with the NullBetween and NullOutside
functions (see Section 3.5., “Other Functions”) to find an optical density at a wavelength
other than max lambda. In addition, the NthItem function can be used to report the OD
at a selected wavelength in the scan (see Section 3.5., “Other Functions” for more information on NthItem).
3.3.
INTERPOLATION FUNCTIONS
Interpolation functions are used to interpolate data from curve fits in Graph sections, and
to access curve fit parameters.
The InterpX, InterpY, and Slope functions are usually used in Group section column formulas (although they are used in specialized Summaries, and the slope function is also
used in Plate section reductions).
The parameter functions—Intercept, ParmA, ParmB, ParmC, ParmD, ParmG and
Rsquared—are usually used in Group or Notes section Summary formulas.
For detailed information on the curve-fit parameters in SoftMax Pro, refer to the SoftMax
Pro User Guide.
Function
Description
AreaUnder(Xvalues,
Returns the trapezoidal area under a curve. This function is
Yvalues)
included as one of the default Kinetic/Spectrum reductions in
Plate and CuvetteSet sections’ Reduction dialog box. It can
also be used in a Summary formula in a Group section.
For example, if “Xvalues” is the name of the list of numbers to
be used for the X values and “Yvalues” is the name of the list
of numbers to be used for the Y values, the formula would
be:
AreaUnder(Xvalues, Yvalues)
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25
3. Functions
Function
Description
AreaUnderFit(PlotName,
Returns the area under the portion of the fit curve defined by
Xstart, Xstop)
the start and stop parameters. The curve is divided into 100
equal ‘slices’ between the start and stop parameters, then the
areas of the trapezoids defined by the ‘slices’ are summed to
determine the area under the curve.
PlotName is the name of the plot for which you want to
determine the area under the curve. Xstart specifies the point
on the X-axis at which to start the area calculation.
Xstop specifies the point on the X-axis at which to stop
calculating the area under the curve.
AreaUnderFit([email protected], 1, 1000)
ChiSquared
Returns the value of the chi-squared statistic from the curve
([email protected] Name)
fit.
[email protected] is the full name of the plot, including
the name of the graph (e.g., Plot#[email protected]#1, or
[email protected]).
ChiProbEx(ChiSquared
Returns the value of the chi-squared probability distribution
([email protected]
for a curve fit with the specified degrees of freedom.
GraphSection),
DegreesOfFreedom is the number of degrees of freedom of
DegreesOfFreedom)
the fit: this is the number of points in the curve minus the
number of fitted parameters in the fit equation.
ChiProbEx(ChiSquared([email protected]), 6)
ChiSquaredPLA
Returns the value of the chi-squared statistic for a reduced
([email protected]
curve fit. This can only be used when Parallel Line Analysis is
GraphSection)
enabled in the Parameter Settings.
The designation of a specific plot is somewhat arbitrary since
the chi-squared value is calculated from all plots in the
designated graph.
ChiSquaredPLA([email protected])
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3.3. Interpolation Functions
Function
Description
ChiProbabilityPLA
Returns the chi-squared probability distribution value for a
([email protected]
reduced curve fit using the appropriate degrees of freedom.
GraphSection)
This can only be used when Parallel Line Analysis is enabled
in the Parameter Settings.
The designation of a specific plot is somewhat arbitrary since
the chi-squared probability is calculated from all plots in the
designated graph.
ChiProbabilityPLA([email protected])
FStatPLA([email protected]
Returns the value of the F-test statistic for a reduced curve fit.
GraphSection)
This can only be used when Parallel Line Analysis is enabled
in the Parameter Settings.
The designation of a specific plot is somewhat arbitrary since
the F-test statistic is calculated from all plots in the designated
graph.
FProbPLA([email protected]
Returns the value of the F-test probability distribution for a
GraphSection)
reduced curve fit using the appropriate degrees of freedom.
This can only be used when Parallel Line Analysis is enabled
in the Parameter Settings.
The designation of a specific plot is somewhat arbitrary since
the F-test probability is calculated from all plots in the graph.
FProbPLA([email protected])
Intercept(Xvalues,
Returns the intercept of a linear regression line that was fit
Yvalues)
(Y=mX+b) to the X and Y values as identified in the function.
Xvalues is the list of numbers to be used for the X values.
Yvalues is the list of numbers to be used for the Y values.
Intercept(Concentration, MeanValue)
InterpX(
Returns the X values of the specified plot interpolated using
[email protected],
the Y values and curve fit.
Yvalues)
[email protected] is the full name of the plot, including
the name of the graph (e.g., Plot#[email protected]#1, or
[email protected]).
InterpX([email protected], YValues)
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27
3. Functions
Function
Description
InterpY(
Returns the Y values of the specified plot interpolated using
[email protected],
the X values and curve fit.
Xvalues)
InterpY(Plot#[email protected]#3, XValues)
ParmA(
Returns the A parameter value of the curve fit assigned to the
[email protected])
specified plot.
ParmB([email protected]
Returns the B parameter value of the curve fit assigned to the
GraphName)
specified plot.
ParmC([email protected]
Returns the C parameter value of the curve fit assigned to the
GraphName)
specified plot.
ParmD([email protected]
Returns the D parameter value of the curve fit assigned to the
GraphName)
specified plot.
ParmG([email protected]
Returns the G parameter value of the 5-parameter logistic
GraphName)
curve fit assigned to the specified plot.
Rsquared([email protected]
Returns the square of the correlation coefficient of the curve
GraphName)
fit assigned to the specified plot.
Slope(Xvalues, Yvalues)
Returns the slope of a line that was fit using linear regression
(Y=mX +b) to the X and Y values specified in the function.
The Slope function is included in the Kinetic Reduction list in
the Reduction dialog for Kenetic runs.
Xvalues is list of numbers to be used for the X values.
Yvalues is the list of numbers to be used for the Y values.
RelativePotency(Standard
Returns the Relative Potency of a Standard compared to a
PlotName, TestPlotName)
Test sample.
When using a 4-parameter curve fit, the Relative Potency is
calculated as the ratio of the C values for the
StandardPlotName curve to the TestPlotName curve.
With a 5-parameter curve fit, the C values are no longer the
mid-point between the max and min. SoftMax Pro
compensates by calculating the IC50 for each plot as:
C×[2^(1/G) - 1]^(1/B)
before taking the ratio.
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3.3. Interpolation Functions
Example: Using InterpX and InterpY in Group Sections
Suppose you have a Graph section named “Graph#1”, in which you have a plot named
“Plot#1”, generated from the X values list Concentration and the Y values list MeanValue:
>
To create a column of interpolated X values, use the formula
InterpX(Plot#[email protected]#1, MeanValue).
>
To create a column of interpolated Y values, use the formula
InterpY(Plot#[email protected]#1, Concentration).
Example: Determining the Slope of the Optical Density versus Time2 for a Kinetic
Plot.
Slope is one of the predefined choices in the list of Kinetic reductions in Plate/CuvetteSet
sections’ Reduction dialog. However, you can also use this function in custom calculations.
For example, you can plot Optical Density versus the square of the Time parameter, and
the slope (i.e., rate) of the line can be calculated using the custom Kinetic reduction:
Slope((!TimeRun)^2, !Lm1)
The reduced plot display for Kinetic plots in Plate or CuvetteSet sections always displays
the results of wavelength combination reductions but not the results of custom Kinetic
reductions. However, the reduced number for custom Kinetic reductions is calculated
using the specified reduction.
Example: Reporting Curve Fit Parameters in Group Section Summaries
The ParmA, ParmB, ParmC, ParmD, and ParmG functions provide a way to export curve
fit parameters with the analyzed data, and also to display the curve-fit parameters to a
greater number of decimal points than are displayed by default in Graph sections.
The ParmC function is particularly interesting as it is the IC50 of a 4-parameter logistic
curve fit with well-defined upper and lower asymptotes.
Example: Determining the Area Under a Plot in a Graph Section
The area under the curve of a plot in a Graph section can be determined using the
AreaUnderFit function. The function generates a series of trapezoids between the X-axis
and the curve, beginning and ending at points on the X-Axis specified by the second and
third parameters of the function. The area within each trapezoid is calculated and then all
of the trapezoidal areas are summed.
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29
3. Functions
3.4.
VMAX REDUCTION FUNCTIONS
You can determine VMax Rate or Time to VMax by using the functions in the Reduction
dialog box. Alternatively, you can use VMax reduction functions to customize VMax
reductions.
All VMax reduction functions require three parameters: all Molecular Devices Microplate
Readers except FlexStation take parameters 1, 2, and 3; FlexStation instruments use
parameters 1, 2, and 4.
First Parameter
The list or array of numbers to be used for the calculation
(e.g.,!CombinedPlot, !WellLm1, !Lm1).
Second Parameter
The number of VMax Points to be used in the calculation. A
constant (e.g., 45) can be entered for the value of this parameter.
If the constant specifies more VMax Points than are contained in
the list or array of numbers specified by the first parameter, then
all points in the list/array will be used. Alternatively, the
!VMaxPoints accessor can be used for this parameter. In this
case, the number of VMax Points specified in the Plate/CuvetteSet
section’s Reduction dialog box is used (see Chapter 4,
“Accessors”).
Third Parameter
The read interval to be used in the calculation. A constant
representing the number of seconds (e.g., 120) can be used for
this parameter. Alternatively, the !ReadInterval accessor can be
used for this parameter, in which case the read interval specified
in the Instrument Settings dialog is used (see Chapter 4,
“Accessors”).
Fourth Parameter
The list of numbers to be used for the calculation. Specifies the
time values, for example, !D3Lm1XVals.
Function
Description
TimeToVMax(Parameter1,
Returns the Time to VMax for the list or array specified by
Parameter2, Parameter3)
the first parameter, based on the number of VMax Points
and the read interval specified in the second and third
parameters, respectively.
30
TimeToVMaxEx(Parameter1,
Returns the Time to VMax for the list or array specified by
Parameter2, Parameter4)
the first parameter, based on the list or array of time values
[FlexStation Only]
specified by the fourth parameter.
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3.4. VMax Reduction Functions
Function
Description
VMax(Parameter1,
Returns the VMax Rate for the list or array specified in the
Parameter2, Parameter3)
first parameter, based on the number of VMax Points and
the read interval specified in the second and third
parameters, respectively.
If you use all of the points in a Kinetic run, VMax is the
same as the slope.
VMaxEx(Parameter1,
Returns the VMax Rate for the list or array specified in the
Parameter2, Parameter4)
first parameter, based on the list or array of time values
[FlexStation Only]
specified by the fourth parameter.
If you use all of the points in a Kinetic run, VMaxEx is the
same as the slope.
VMaxCorr(Parameter1,
Returns the correlation coefficient for the VMax Rate of the
Parameter2, Parameter3)
list or array specified in Parameter1, based on the number
of VMax Points and read interval specified by the second
and third parameters, respectively. It can be used to
display this value as the reduced number in a Plate section
or as a column in a Group section.
VMaxCorrEx(Parameter1,
Returns the correlation coefficient for the VMax Rate of the
Parameter2, Parameter4)
list or array specified in Parameter1, based on the list or
[FlexStation Only]
array of time values specified by the fourth parameter. It
can be used to display this value as the reduced number in
a Plate section or as a column in a Group section.
VMaxPerSec(Parameter1,
Returns the VMax Rate (in seconds) for the list or array
Parameter2, Parameter3)
specified by the first parameter based on the number of
VMax Points and the read interval specified in the second
and third parameters, respectively.
If you use all the points in a Kinetic run, VMaxPerSec is the
same as the slope.
VMaxPerSecEx(Parameter1,
Returns the VMax Rate (in seconds) for the list or array
Parameter2, Parameter4)
specified by the first parameter, based on the list or array
[FlexStation Only]
of time values specified by the fourth parameter.
If you use all the points in a Kinetic run, VMaxPerSecEx is
the same as the slope.
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31
3. Functions
Function
Description
VMaxPtsUsed(Parameter1,
Returns the number of points that will be used to calculate
Parameter2, Parameter3)
the VMax for the list or array specified in the first
parameter, based on the number of VMax Points and the
read interval specified in the second and third parameters,
respectively.
VMaxPtsUsedEx(Parameter1
Returns the number of points that will be used to calculate
, Parameter2, Parameter4)
the VMax for the list or array specified in the first
[FlexStation Only]
parameter, based on the list or array of time values
specified by the fourth parameter.
Example: Viewing VMax Rate Determined Using Different Numbers of VMax Points
in Columns of a Group Section
You can calculate VMax Rate using different numbers of VMax points. For example, you
can create columns named VMax45, VMax25, VMax10, and VMax5 using variations on
the custom formula:
VMax(!WellCombinedPlot, 45, !ReadInterval)
with the VMax Points set to 45, 25, 10, or 5, respectively. !WellCombinedPlot specifies
the list of numbers to be used to calculate the VMaxRate (see Section 4.3., “Plate Data
Accessors” for a complete discussion of the !WellLx accessors), and the !ReadInterval accessor specifies that the read interval defined in the Instrument Settings dialog is used in the
calculation.
Using fewer VMax Points allows SoftMax Pro to calculate the linear regression of subsets
of the data in each well using creeping iteration, then report the fastest rate (i.e., the steepest slope) in each well. For a complete description of how VMax Points are used, and how
VMax Rate is calculated, please see the SoftMax Pro User Guide.
Example: Viewing the VMax Correlation Coefficient as a Plate Reduction
To display the VMax Correlation Coefficient as a plate reduction:
1 In the Display dialog box choose to plot raw data with reduced number.
2 In the Reduction dialog box, select Custom for the kinetic reduction.
3 Enter the following formula:
VMaxCorr(!CombinedPlot, !VMaxPoints, !ReadInterval)
The reduced number is the correlation coefficient of the VMax Rate (or slope) calculation.
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3.4. VMax Reduction Functions
Example: Viewing the VMax Correlation Coefficient as a Column Reduction with
the VMax Rate
If Kinetic data is collected in a Plate section whose Reduction dialog box was used to set
the reduction to VMax Rate, using the accessor !WellValues can bring the reduced number from the Plate section into the Group section.
The VMax Correlation Coefficient has the custom formula:
VMaxCorr(!WellCombinedPlot, !VMaxPoints, !ReadInterval)
The formula’s first parameter, !WellCombinedPlot, identifies the list that should be calculated for the VMax correlation coefficient, !VMaxPoints specifies the use of the VMax
Points as defined in the Reduction dialog, and !ReadInterval directs the formula to use the
Read Interval specified in the Instrument Settings dialog.
The !WellLm1, !VMaxPoints, and !ReadInterval accessors are discussed in detail in
Chapter 4, “Accessors”.
Example: Viewing the Number of VMax Points Used to Calculate Each VMax Rate in
a Group Section Column
If a number is used to specify how many VMax Points should be used when calculating
the VMax Rate, that number of VMax Points is used if that many data points are visible
in the well/cuvette plot in the Plate/CuvetteSet section.
However, if the number of visible data points is less than the specified number of VMax
Points, only the number of points that are visible are used (for a complete discussion of
how VMax Rate is calculated, see the SoftMax Pro User Guide.)
This example demonstrates how to employ the VMaxPtsUsed accessor to determine the
actual number of VMax Points that are used in determining the VMax Rate:
VMaxPtsUsed(!WellLm1, !VMaxPoints, !ReadInterval)
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33
3. Functions
3.5.
OTHER FUNCTIONS
The functions listed below allow you to access individual items within lists of numbers, to
eliminate portions of lists from the calculation, and to take the difference (delta) between
time points of a Kinetic run. These functions are generally used in conjunction with other
functions and accessors.
Function
Count(Parameter)
Description
Returns the count of items in a list of numbers.
Count(list) = 5
This function does not count empty or error values in the
list.
Delta(Parameter)
Returns a list of the deltas (differences) between adjacent
points in a list. For a list named ‘Values’, the formula is:
Delta(Values)
FirstArray(Parameter)
Reports the first array in a list of arrays. The returned
values can be numbers, text, or booleans.
FirstArray(!WellLm1)
FirstItem(Parameter)
Reports the first item in a list or array of numbers (e.g., the
first OD in a Kinetic run, the first OD in a Spectrum scan,
the first value in a column of numbers).
FirstItem(!CombinedPlot)
Index
Returns an index for the samples in a group, going from 1
to n, for n samples.
Index
IndexListFor(Parameter) or
Results in an index for a list or array of numbers (i.e., for
ItemIndex(Parameter)
the list 123, 125, 130, 127... the index is 1=123, 2=125,
3=130, 4=127...)
IndexListFor(Values)
IndexofMax(Parameter)
Reports the index of the maximum of a list or array of
numbers.
IndexofMax(Results)
IndexofMin(Parameter)
Reports the index of the minimum of a list or array of
numbers.
IndexofMin(Results)
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3.5. Other Functions
Function
Description
IndexofNearest(Parameter1,
Parameter1 is a list or array of numbers. Parameter2 is a
Parameter2)
numerical value. The function returns the index of the
number in Parameter 1 that is closest to the value of
Parameter2.
IndexofNearest(!CombinedPlot, 5)
Item(Parameter1,
Parameter1 is a list of numbers. Parameter2 is a numerical
Parameter2)
value. The function returns the value of the specified item
in the list.
Item(Values,2)=25
ItemCount(Parameter) or
Returns the count (or number of items) of items in a list or
Count(Parameter)
array of numbers, text items, or booleans. The function
does not count empty or error values in the list.
ItemCount(Values)
NearestTo(Parameter1,
Parameter1 is a list or array of numbers. Parameter2 is a
Parameter2)
numerical value. The function returns the value of the
number in Parameter 1 that is closest to the value of
Parameter2.
NearestTo(Values, .5)
NthArray(Parameter1, N)
Parameter1 is a list of arrays. N is a number. The function
returns the ‘Nth’ array in Parameter1. The array can
contain numbers, text, or booleans.
NthArray(!WellLm1, 8)
NthItem(Parameter1, N) or
Parameter1 is a list or array of numbers. N is a number.
Item(Parameter1, N)
The function returns the value of the ‘Nth’ item in
Parameter1.
NthItem(!Lm1, 50)
NullBetween(Parameter1,
Omits selected items in a list or array of numbers by
Parameter2, Parameter3)
setting their value to the “empty” NAN. Parameter1 is the
list/array of numbers to be acted on, Parameter2 is a
number indicating at which item in the list/array to begin
omitting, and Parameter3 is a number indicating at which
item in the list/array to stop omitting. Items between the
points indicated by parameters 2 and 3 will be omitted.
NullBetween(!WellLm1, 50, 100)
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35
3. Functions
Function
Description
NullOutside(Parameter1,
Omits selected items in a list or array of numbers by
Parameter2, Parameter3)
setting their value to the “empty” NAN. Parameter1 is the
list/array of numbers to be acted on, Parameter2 is a
number indicating at which item in the list/array to stop
omitting, and Parameter3 is a number indicating at which
item in the list/array to resume omitting. Items not
between the points indicated by parameters 2 and 3 will
be omitted.
NullOutside(!WellLm1, 50, 100)
Sideways(Parameter)
In a Group section, takes lists or arrays of numbers that
would normally be reported in a vertical column and
reports them in a horizontal row.
Sideways(!Timerun)
Example: Using NullBetween and NullOutside to Show Selected Portions of Kinetic
Data
You can use the NullBetween and NullOutside functions to create new columns containing selected data, then plot the new columns in a Graph section and determine the slope
of the data there.
For example, you can retrieve selected data from wells A1, A2 and A3 as follows:
WellA1: NullOutside([email protected]#1, 10, 20)
WellA2: NullOutside([email protected]#1, 15, 20)
WellA3: NullBetween([email protected]#1, 10, 34)
The NullOutside function excludes items in the list below the value indicated by the second parameter and above the value indicated by the third parameter. Thus, in the formula
for column WellA1, the first parameter is !A1Lm1 (the optical densities collected at each
time point in well A1), the second parameter is 10 (i.e., the 10th time point collected) and
the third parameter is 20 (i.e., the 20th time point collected). Column WellA1 therefore
includes points 11-19 only, while WellA2 includes points 16-19 only.
The NullBetween function excludes all items in the list between (and including) the second and third parameters. Thus, in the formula for column WellA3, the list of numbers is
!A3Lm1 (the optical densities collected at each time point in well A3) and data points 10
through 34 are excluded from the data analysis.
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3.5. Other Functions
In this example, the columns are reporting data directly from the wells in the Plate section
rather than using the “template order” normally used in Group sections. Use formulas of
this type with caution.
Example: Using IndexOfMax with NullOutside to Determine Multiple Peaks in a
Spectrum Scan
To look for three peaks in a Spectrum scan, you can create three column formulas named
Peak1, Peak2 and Peak3. The formulas for the columns named Peak1, Peak2, and Peak3
are the same except for the second and third parameters of the NullOutside function. The
formula for the column named Peak1 is:
(IndexOfMax(NullOutside(!WellLm1, 20, 40))-1) * [email protected]#1 +
[email protected]#1
The formula reports the index of the maximum item in the list of numbers named
!WellLm1 (which contains an array of all Spectrum scan optical densities from each well,
reported in template order).
For each list included in the array, the formula ignores everything below item 20 (i.e., the
OD at the 20th wavelength in the scan) and above item 40 (i.e., the OD at the 40th wavelength in the scan). Once IndexOfMax is calculated, the formula subtracts 1 and then
multiplies the result by the sweep increment (!StepSweep, specified in the Instrument Settings dialog) and adds the wavelength at which the Spectrum scan started (!StartSweep,
also specified in the Instrument Settings dialog).
The !StepSweep and !StartSweep accessors are discussed in detail in Section 4.2., “Kinetic
and Spectrum Data Accessors”.
Example: Calculating the First Derivative of a Kinetic Plot
Generally, when calculating the reaction rate of a Kinetic run (the VMax Rate), you are
determining the slope of the line that results from plotting change in OD vs. Time. However, in some situations you may wish to calculate the slope of the line that results when
you plot the delta (i.e., the rate of change) in the ODs vs. Time. The slope of this line is
the first derivative of the Kinetic plot, and can be calculated as follows:
VMax(Delta(!KinPlot), !VMaxPoints, !ReadInterval)
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37
3. Functions
3.6.
NANS/MAKEERRS
SoftMax Pro contains a special class of numbers called NANs (Not A Number) that are
used to report errors and special values. NANs are special because, although they appear
to be text, they are actually numbers. Because NANs are numbers, numerical calculations
can be performed on lists or arrays of numbers that contain NANs.
NANs propagate through most operations and functions in SoftMax Pro.
SoftMax Pro uses some of the NANs to report errors/other messages in Plate or
CuvetteSet sections, Group sections, and Graph sections.
Other NANs are only used by the user when creating custom formulas.
NAN
MakeErr(101)
Returns
“”
An empty number.
MakeErr(102)
“Name?”
MakeErr(103)
“Masked”
Usually seen in a Group section column when wells in a Plate or
CuvetteSet section have been masked.
MakeErr(104)
“NoFit”
Usually seen in Graph section when no fit has been chosen from
the list of curve fits.
MakeErr(105)
“FitError”
Usually seen in Graph section when SoftMax Pro is unable to
apply the chosen curve fit to the data set.
MakeErr(106)
“Range?”
MakeErr(107)
“?????”
For use in custom formulas.
MakeErr(108)
“Error”
MakeErr(109)
“Domain”
Internal program use.
MakeErr(110)
“PrLoss”
Internal program use.
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3.6. NANs/MakeErrs
NAN
MakeErr(111)
Returns
“Path?”
Seen in Plate sections when PathCheck is selected and the preread has been performed, but the normal read hasn’t yet been
performed. Also seen if SoftMax Pro was unable to perform the
PathCheck calculation after the normal read.
MakeErr(112)
“Open?”
Cuvette door was open.
MakeErr(113)
“Limits-“
Out of reduction limits.
MakeErr(114)
“Limits+”
Out of reduction limits.
MakeErr(115)
“Pass”
For use in custom formulas.
MakeErr(116)
“Fail”
For use in custom formulas.
MakeErr(117)
“High”
For use in custom formulas.
MakeErr(118)
“Low”
For use in custom formulas.
MakeErr(119)
“>>>>>”
For use in custom formulas.
MakeErr(120)
“<<<<<”
For use in custom formulas.
MakeErr(121)
“+++++”
For use in custom formulas.
MakeErr(122)
“- - - - -“
For use in custom formulas.
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39
3. Functions
NAN
MakeErr(123)
Returns
“*****”
For use in custom formulas.
MakeErr(124)
“&&&&”
For use in custom formulas.
MakeErr(125)
“#Low”
For use in custom formulas.
MakeErr(124)
“#Sat”
For use in custom formulas.
The following list contains the functions that can be used to manipulate NANs:
Function
NoNum
Description
Takes no parameters. Returns an “empty” number. It is the same
as MakeErr(101).
IsEmpty(Parameter)
Returns true if a number, list of numbers, or array of numbers is
empty; otherwise returns false.
IsErr(Parameter)
Returns true if a number, list of numbers, or array of numbers is a
NAN; otherwise returns false.
WhatErr(Parameter)
Returns which error the NAN represents (see list in previous table)
or 0 if the number, list of numbers, or array of numbers is not a
NAN.
MakeErr(Parameter)
Creates a value corresponding to the list of NANs above.
The following examples use NANs in formulas. NANs are rarely, if ever, used by themselves. However, frequently they are used as part of conditional statements.
Example: Using NANs to Create a Pass/Fail Column
Using NANs allows you to combine text with numbers in a column. In this example, we
create a column that reports either the optical density or “Fail”, depending on the value of
the optical density. Since SoftMax Pro treats NANs as if they are numbers, further calculations can be performed on this column, even though it appears to contain a string. The
formula is a simple conditional statement:
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3.7. Text Functions
If (Values >= MeanValue-(0.2*MeanValue) and Values <= MeanValue+
(0.2*MeanValue), Values, MakeErr(116))
Example: Using NANs in a Plate Section
You can use NANs in custom reduction formulas in the Reduction dialog for a Plate section. For example, you can use the following conditional statement that returns the NAN
MakeErr(118) (“Low”) if the optical density in a well is below the optical density in well
A12, to return the NAN MakeErr(117) (“High”) if the optical density is higher than the
OD in well H1, and to report the optical density if it is between the ODs in wells A1 and
H1:
If(!Lm1 < !A12, MakeErr(118), (If (!Lm1>!H1, MakeErr(117), !Lm1)))
3.7.
TEXT FUNCTIONS
The following functions allow you to manipulate text strings in SoftMax Pro.
Function
ASCII(“Text”)
Description
Returns the ASCII value for the first character in the text string.
ASCII(“Average”) = 65
Concat(“Text1”,
Concatenates a series of text strings together. This may also be
“Text2”…”TextN”)
done using the + operator (see Section 2.1., “Mathematical
Operators” for more on the + operator).
Concat(“Molecular”, “Devices ”, “Corporation”) = Molecular
Devices Corporation
Exact(“Text1”,
Returns true if the two text strings are identical and false if they
“Text2”)
are not.
Note: This function is case sensitive. To do a case insensitive
comparison, use the “=” operator.
Exact(“Softmax Pro”, “SoftMax Pro”) = False
Exact(“SoftMax Pro”,“SoftMax Pro”) = True
Left(“Text”, N)
Returns the first N characters from the left end of a text string.
Left(“SoftMax Pro”, 4) = “Soft”
Right(“Text”, N)
Returns the first N characters from the right end of text string.
Right(“SoftMax Pro”, 3) = “Pro”
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41
3. Functions
Function
Mid(“Text”, N1, N2)
Description
Returns the text between the specified start and stop characters.
Mid(“SoftMax Pro”, 5, 3) = “Max”
Len(“Text”)
Returns the length of (or number of characters in) the text string.
Len(“Molecular Devices”) =17
Lower(“Text”)
Returns the text in all lower-case characters.
Lower (“Molecular Devices”) = “molecular devices”
Upper(“Text”)
Returns the text in all uppercase characters.
Upper (“SoftMax Pro”) = “SOFTMAX PRO”
Text
Converts numbers to text—returns a number, list of numbers, or
(NumericalParameter)
array of numbers as text strings.
Text(26.00) = “26”
Val(“Text”)
Returns a number corresponding to the numerical value of the
beginning of the text string. If the beginning of the string is not a
number, it returns 0.
Val(“24”) = 24.00
Val(“24.4, 4asfg”) = 24.4
Val(“abcd24.4”) = 0.0
Now
Takes no parameters. Returns the current time of day.
Note: Every time you open or recalculate the file, Now will be
updated to the current time.
Now = 9:05:30 AM
Today
Returns the current day and date.
Note: Every time you open or recalculate the file, Today will be
updated to the current day and date.
Today = Friday, April 29, 2005
Example: Combining Text with Numbers to Report a Results Column
In some situations, you may wish to flag certain results in a column and need to have the
flag and the numerical results in the same column. One way to accomplish this is by converting the numbers to text.
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3.7. Text Functions
Keep in mind that after SoftMax Pro converts numbers to text, no further calculations can
be performed on the numbers.
We can construct a new column from the column “Adj.Result” as follows:
If (Adj.Result<0, “***” + Left((Text(Adj.Result)), 6) + “***”, Left((Text(Adj.Result)),
6))
The conditional statement specifies:
>
If the adjusted result is less than zero, report ***text string***.
>
If not, report text string.
In both cases, the text string is defined as Left((Text(Adj.Result)), 6), because when a column of numbers is turned into text, the numbers are reported to a large number of decimal places. Therefore, the formula uses the Left function to limit the display of the text
string to the 6 leftmost characters.
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3. Functions
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4. Accessors
Accessors are special functions that provide access to other SoftMax Pro-specific information (for example, the number of VMax Points used to calculate the VMax Rate). Unlike
functions, accessors do not have parameters associated with them. Accessors are always
preceded by an exclamation point (!, also known as a “bang”).
Accessors are frequently used by themselves as column formulas. They are also used as
parameters within several functions, most notably kinetic and Spectrum reduction functions. Accessors can also be combined with functions and mathematical operators to create complex formulas.
Accessors can be divided into several broad categories:
>
Plate/CuvetteSet section information accessors
>
Kinetic/Spectrum information accessors
>
Plate/CuvetteSet data accessors
>
Group information accessors
>
Well information accessors
>
Blank data accessors.
Using “Well” as an Accessor Prefix
Accessors can refer to the information in Plate/CuvetteSet sections within SoftMax Pro in
two ways: in read order (well A1, A2, A3,A4…) or in template or group order (wells
A1,B1,A2,C2 from Plate#1 and wells G1,H1,G2,H2 on Plate #2 if they are part of the
same group). When the word “Well” is used as a prefix between the exclamation point and
the accessor, the information is reported in group order:
!Accessor
!WellAccessor
!WellAccessor is used ONLY in Group sections and !Accessor is almost never used in
Group section tables.
The “Well” prefix is not valid with all accessors (accessors that can be used with Well are
noted in the sections below).
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45
4. Accessors
4.1.
PLATE/CUVETTESET SETUP INFORMATION ACCESSORS
Plate/CuvetteSet section information accessors provide information about Plate or
CuvetteSet section settings. Following the listing of these accessors and their descriptions
is a series of examples showing how to use these accessors.
Accessor
!AutoCutoffOn
!WellAutoCutoffOn
Description
Returns True if the emission cutoff filter is set to
Automatic in the Instrument Settings dialog and reports
False if the emission cutoff filter is set to manual.
[Fluorescence mode only.]
!AvgReadTemperature
!WellAvgReadTemperature
!EmCutoffs
!WellEmCutoffs
Returns (as a number) the average temperature
measured while the plate or cuvette was read.
Reports the cutoff filter wavelengths set in the
Instrument Settings dialog for Endpoint, Kinetic, and
Spectrum reads.
[Fluorescence mode only.]
!EmFixedWavelength
!WellEmFixedWavelength
Reports the wavelength at which emission is fixed when
performing an excitation scan. If the emission
wavelength is not fixed, no number is reported.
[Fluorescence mode only.]
!EmWavelengths
!WellEmWavelengths
[Fluorescence mode only.]
Reports the emission wavelength(s) chosen in the
Instrument Settings dialog for Endpoint, Kinetic, and
Spectrum reads. All (i.e., white light) is the default
emission wavelength for luminescence assays and is
returned unless a specific emission wavelength is
chosen.
!ExFixedOn
!WellExFixedOn
Reports True if the instrument setting is set to perform a
Spectrum scan with fixed excitation and variable
emission wavelengths.
[Fluorescence mode only.]
!ExFixedWavelength
!WellExFixedWavelength
Reports the wavelength at which excitation is fixed
when performing an emission scan. If the excitation
wavelength is not fixed, no number is reported.
[Fluorescence mode only.]
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Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
4.1. Plate/CuvetteSet Setup Information Accessors
Accessor
!ExWavelengths
!WellExWavelengths
Description
Reports the excitation wavelengths specified in the
Instrument Settings dialog for Endpoint, Kinetic, and
Spectrum reads.
[Fluorescence mode only.]
!FirstColumn
!WellFirstColumn
!Gfactor
Returns (as a number) the first column read in a
specified Plate section. Useful when reading only
selected columns on a plate.
Returns the current Gfactor value set in the Display
dialog box.
!IntegrationEnd
Returns (as a number) the integration end time.
!WellIntegrationEnd
[Time Resolved Fluorescence
mode only]
!IntegrationStart
Returns (as a number) the integration start time.
!WellIntegrationStart
[Time Resolved Fluorescence
mode only]
!LastColumn
!WellLastColumn
!NumWells
!WellNumWells
Returns (as a number) the last column read in a
specified Plate section. Useful when reading only
selected columns on a plate.
Returns the number of wells in the plate type specified
in the Instrument Settings dialog.
[Fluorescence mode only.]
!PlateName
!WellPlateName
Returns the name of the Plate/CuvetteSet section as a
text string. This accessor is very useful when Group
sections contain samples from multiple plates in which
the samples are in the same wells since it reports which
plate the sample was in.
!PlateType
!WellPlateType
Returns the text string “Endpoint”, “Kinetic”, or
“Spectrum” depending on the instrument setup.
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47
4. Accessors
Accessor
!PMTSetting
!WellPMTSetting
Description
Returns the text string “Automatic”, “High”, “Medium” or
“Low” depending on the PMT Setting chosen in the
Instrument Settings dialog.
[SpectraMax Gemini, M2,
M2e, M5 and M5e in
Fluorescence mode only.]
!PreMixDuration
!WellPreMixDuration
Returns the number of seconds Automix has been set to
mix prior to reading in the Instrument Settings dialog.
For Kinetic runs, it reports the Automix duration prior to
the first read. It does not report the Automix duration inbetween reads (Section 4.2., “Kinetic and Spectrum
Data Accessors”).
!PreMixOn
!WellPreMixOn
Returns True if Automix has been turned on in the
Instrument Settings dialog box and False if Automix has
not been turned on. (For Kinetic runs, this applies to
Automix prior to the first read. For Automix between
reads, see Section 4.2., “Kinetic and Spectrum Data
Accessors”).
!PreReadOn
!WellPreReadOn
!ReadsPerWell
!WellReadsPerWell
Returns True if the Pre-Read Instrument setting has
been checked in the Instrument Settings dialog box;
returns False if it has not been turned on.
Returns (as a number) the reads per well specified in the
Instrument Settings dialog box.
[Fluorescence mode only.]
!ReadType
!WellReadType
Returns the text string “Absorbance”, “Fluorescence”,
“Luminescence”, or “Time Resolved”, depending on the
instrument setup.
[Not available on all
instruments]
!TemperatureSetPoint
!WellTemperatureSetPoint
!TimeOfRead
!WellTimeOfRead
48
Returns (as a number) the incubator set point (from the
Instrument Settings dialog box) at the time the plate or
cuvette was read.
Returns the time and date the plate or cuvette was read
(this information can be found in the time/date stamp
displayed in Plate/CuvetteSet sections after a reading).
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
4.2. Kinetic and Spectrum Data Accessors
Accessor
Description
!TimeResolvedOn
Returns True if the Read Mode in the Instrument
!WellTimeResolvedOn
False if the Read Mode is not set to Time Resolved.
Settings dialog box is set to Time Resolved. Reports
[Time Resolved Fluorescence
mode only.]
!Wavelengths
!WellWavelengths
Returns as a text string (e.g., “405 650”) the
wavelength(s) at which a Plate/CuvetteSet section was
read.
Example: Using Plate Information Accessors in Summary Lines
If a data file contains data from more than one plate, you can report the start and end
time of the experiment using !TimeOfRead. If the first plate read was PlateX and the last
plate was PlateY, the following two formulas return the start and end time, respectively:
[email protected]
[email protected]
The information is being reported directly from the Plate sections, so “Well” is not used
in the accessors.
4.2.
KINETIC AND SPECTRUM DATA ACCESSORS
The accessors in the following table are specific to Kinetic and/or Spectrum scan data.
They allow you to:
>
Access information about the run and customize analysis of Kinetic or Spectrum data.
>
Manipulate both the Y-axis information (OD) and the X-axis information (time for
Kinetic runs, wavelength for Spectrum scans).
Accessor
!NumPoints
Description
Returns the number of data points (number of time
points to be collected in a Kinetic run or number of
!WellNumPoints
wavelengths to be read in a Spectrum scan) specified in
the Instrument Settings dialog Box.
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49
4. Accessors
Accessor
!NumPointsRead
!WellNumPointsRead
[SpectraMax Plus,
SpectraMax 190, SpectraMax
340 PC, VersaMax,
SpectraMax Gemini only]
Description
Returns the actual number of time points during which
data was collected. This accessor is very useful if you
have stopped a Kinetic run sooner than was specified in
the Instrument Settings.
This accessor returns both numbers and NANs and,
thus, it may not detect missing data points in a Kinetic
run or Spectrum scan due to low light. If you want to
detect missing data points, use the ItemCount function.
!NumWavelengthsRead
!WellNumwavelengthsRead
Returns the actual number of wavelengths that are read
in an Endpoint run or Spectrum scan. This accessor is
very useful when you have stopped a Spectrum scan
before the end wavelength (selected in the Instrument
Settings dialog box) is read.
The information reported by this accessor is invalid for
Endpoint readings if PathCheck has been selected in the
Instrument Settings dialog box.
!ReadInterval
!WellReadInterval
!RunTime
!WellRunTime
Returns the number of seconds specified in the
Instrument Settings dialog box for a Kinetic run read
interval.
Returns the time (in seconds) that it will take to read a
Kinetic plate, as calculated from the information in the
Instrument Settings dialog box.
If the run is terminated before it can be completed, this
accessor will still report the calculated time to finish the
run, not the actual run time (however, !WellNumPoints
could be used to calculate the actual number of data
points collected).
!StartSweep
!WellStartSweep
!EndSweep
!WellEndSweep
!StepSweep
!WellStepSweep
50
Returns (as a number) the wavelength at which to begin
a Spectrum scan as specified in the Instrument Settings
dialog box.
Returns (as a number) the wavelength at which to end a
Spectrum scan as specified in specified in the
Instrument Settings dialog box.
Returns (in nm) the step size of a Spectrum scan as
specified in the Instrument Settings dialog box.
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
4.2. Kinetic and Spectrum Data Accessors
Accessor
Description
!AutomixOn
Returns (as a text string) True if Automix between reads
!WellAutomixOn
dialog box and False if it is not checked.
!AutomixDuration
Returns the number of seconds set for Automix
!WellAutomixDuration
!TemperatureRun
!WellTemperatureRun
is checked for Kinetic plates in the Instrument Settings
between Kinetic reads as specified in the Instrument
Settings dialog box.
Returns a list of numbers that contains temperature data
collected during the read. One temperature is reported
for all wells at each time point.
This accessor can be used for Endpoint reads as well as
for Kinetic runs and Spectrum scans. It is very useful for
plotting the effects of temperature on your data.
!TimeRun
!WellTimeRun
!TimeRun returns a list of read times in a vertical
column.
!WellTimeRun returns a list of read times in a horizontal
array. Valid for use with Kinetic data only, this accessor
returns a list of numbers corresponding to the times at
which Kinetic data points are collected.
Although the individual wells of a 96-well plate are read
fractions of a second apart during each time point in a
Kinetic read, the same time point is reported for all wells
(e.g., if a series of wells is read at 9, 9.1, and 9.2
seconds, and then read again at 12, 12.1, and 12.2
seconds, the !TimeRun accessor will return 9 and then
12 for the read times). All of the cuvettes in a CuvetteSet
section also report the same time points because,
although the Kinetic read on each cuvette is started at a
different time, the accessor reports the elapsed time
during the read.
!WavelengthRun
!WellWavelengthRun
Returns (as a list of numbers) the wavelengths at which
each of the Spectrum scan data points are collected.
Note: This accessor is valid for Spectrum scans only.
!MinLimit
!WellMinLimit
Returns (as a number) the Min OD set in the Reduction
dialog for a Spectrum scan or Kinetic run. Any data
collected below the Min OD will be reported with the
NAN MakeErr(113) “Limits-” and will not be used in any
reduction.
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51
4. Accessors
Accessor
!MaxLimit
!WellMaxLimit
Description
Returns (as a number) the Max OD set in the Reduction
dialog for a Spectrum scan or Kinetic run. Any data
collected above the Max OD will be reported with the
NAN MakeErr(114) “Limits+” and will not be used in any
reduction.
!StartLimit
!WellStartLimit
Returns (in seconds) the lag time for Kinetic run data
analysis and the start wavelength for Spectrum scans
(both set in the Reduction dialog box). Any data
collected before the lag time or below the starting
wavelength is reported with the NAN MakeErr(113)
“Limits-” and is not used in any reduction.
!EndLimit
!WellEndLimit
Returns the end time set for Kinetic run data analysis
and the end wavelength set for Spectrum scan data
analysis (both set in the Reduction dialog box). Any data
collected after the end time or above the end
wavelength is reported with the NAN MakeErr(114)
“Limits+” and is not used in any reduction.
!VMaxPoints
!WellVMaxPoints
Returns the number of points that would be used to
calculate VMax if the reduction were set to VMax. The
accessor reports the number of VMax Points set in the
Reduction dialog (the default is total number of time
points collected during a Kinetic run). To determine the
actual number of VMax Points used in each well, use the
VMaxPtsUsed reduction function.
!OnsetValue
!WellOnsetValue
[Previously called !OnsetOD,
Returns (as a number) the onset value (OD, RFU, RLU)
specified in the Reduction dialog to be used in
calculating Onset Time if the reduction is set to Onset
Time.
!WellOnsetOD]
!XVals
Returns the values associated with the X-axis of a
Kinetic or Spectrum read. This is the same as !TimeRun
for Kinetic data or !WavelengthRun for Spectrum data.
Example: Accessing Kinetic Run Settings Information
The !NumPoints and !NumPointsRead accessors can be used to determine the number of
points specified for a Kinetic run and the number of points actually collected if the run is
stopped early. The same information can be determined for a Spectrum scan by using the
!NumPoints and !NumWavelengthsRead accessors.
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4.2. Kinetic and Spectrum Data Accessors
We can create a column to calculate the actual number of VMax Points used in each well
to calculate the rate of the reaction with the formula:
VMaxPtsUsed(!WellLm1, [email protected]#1, [email protected]#1)
We can also create Summaries to report the original settings and the actual number of
readings.
Number of time points configured in Instrument Settings:
!NumPoints
Number of time points collected during Kinetic run:
!NumPointsRead
Run time configured in Instrument Settings:
!RunTime
Actual run time during Kinetic run:
NthItem(!TimeRun, !NumPointsRead)
This last formula returns the time at which the last data point was collected (i.e., the run
time).
Example: Summarizing Spectrum Scan Parameters Using Summaries
Starting wavelength of the Spectrum scan:
!StartSweep
Ending wavelength of the Spectrum scan:
!EndSweep
Step increment in nm of scan:
!StepSweep
Starting wavelength of data analysis:
!StartLimit
End wavelength of data analysis:
!EndLimit
If more than one Plate section or CuvetteSet section is present in the Experiment section
you need to identify the Plate/CuvetteSet section in the formulas; for example,
[email protected]#1 or [email protected]#1.
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53
4. Accessors
Example: Temperature, Time, and Wavelength Information from Kinetic
Plots/Spectrum Scans
If the Well prefix is used with the !TemperatureRun, !TimeRun, and !WavelengthRun
accessors in Group sections, the lists of numbers are reported in the Group section as a
horizontal array. When information is displayed in this fashion, you may perform further
mathematical manipulations on the array of numbers but you may not plot it in a Graph
section.
You can also access temperature, time, and wavelength information in a Group section
independently of the template. If you do so, the information will be placed in a column,
and you can graph optical density versus temperature, time, or wavelength; time versus
temperature; or wavelength versus temperature.
4.3.
PLATE DATA ACCESSORS
Plate data accessors allow you to access optical density (raw data), reduced numbers, preread data, and pathlength correction information from Plate sections, CuvetteSet sections,
and Group sections. These accessors can be used in Plate sections, CuvetteSet sections,
and Group sections.
Accessor
!LmX
!A1LmX
!WellLmX
Description
Reports (as a number, in Endpoint readings, or list of
numbers, in Kinetic/Spectrum scans) the raw OD values
(before the wavelength combination reduction is
applied) from wells or cuvettes.
LmX specifies the wavelength (i.e., Lm1, Lm2, etc.).
!LmX accesses the raw values from all wells or cuvettes
in the section at the given wavelength.
!A1LmX accesses the raw value from the specified well
or cuvette at the specified wavelength (for example,
!H2Lm1, or !B12Lm3).
!WellLmX accesses the raw optical densities reported in
a Group section in template order. Optical densities at
each Kinetic run time point or each Spectrum scan
wavelength are reported in a horizontal array.
!WellLmXSRaw
(For Fluorescence
Polarization readings only)
Reports the raw values (before any other reduction is
applied) from wells or cuvettes for perpendicular
polarized data of a specific wavelength (e.g., Lm1 or 1st
wavelength set) for a given template group (in a Group
section). !WellLmXSRaw accesses the raw values
reported in a Group section in template order.
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4.3. Plate Data Accessors
Accessor
!WellLmXPRaw
(For Fluorescence
Polarization readings only)
Description
Reports the raw values (before any other reduction is
applied) from wells or cuvettes for parallel polarized
data of a specific wavelength (e.g., Lm2 or
2ndwavelength set) for a given template group (in a
Group section). !WellLmXPRaw accesses the raw values
reported in a Group section in template order.
!WellIDLmXSRaw
(For Fluorescence
Polarization readings only)
!WellIDLmXPRaw
(For Fluorescence
Polarization readings only)
!A1LmXXVals
!WellLmXXVals
Returns perpendicular (or an array of perpendicular)
data for the given well (e.g., A2) and specified
wavelength (e.g., Lm1 or 1st wavelength set).
Returns parallel (or an array of parallel) data for the
given well (e.g., A2) and specified wavelength (e.g., Lm1
or 1st wavelength set).
Reports (as a list of numbers, in Fast Kinetic scans) the
actual read time (time-tagged) values from wells. LmX
specifies the wavelength (i.e., Lm1, Lm2, etc.). In Plate
sections, !A1LmXXVals returns the read time (timetagged) for the specified well at the indicated
wavelength. !WellLmXXVals accesses the actual read
time reported in a Group section in template order. The
read time (time-tagged) data will be reported in a
horizontal array. This accessor is valid only for
FlexStation.
!AllWavelengths
!WellAllWavelengths
Returns (as a list of numbers) the raw optical densities
for each wavelength read in a given well. This accessor
can only be used with multiple-wavelength Endpoint
reads.
!Values
!WellValues
Returns the reduced number from each well of a Plate
section or cuvette in a CuvetteSet section. !WellValues is
the default formula given to the default Group sections
column named Values.
!MValue
!Pvalue
(Not available on all
instruments)
Returns the reduced number from each well of a Plate
section or cuvette in a CuvetteSet section. !MValue is
returned as the default for readings taken after an Minjection; !PValue is returned as the default for readings
taken after an P-injection.
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55
4. Accessors
Accessor
!AllValues
Description
Returns a list of the reduced numbers from all wells in a
Plate section or all cuvettes in a CuvetteSet section.
!PreReadLmX
!A1LmXPreRead
!WellPreReadLmX
Reports (as a number, in Endpoint readings, or list of
numbers, in Kinetic/Spectrum scans) the pre-read
values from wells or cuvettes. LmX specifies the
wavelength (i.e., Lm1, Lm2, etc.).
In Plate sections !PreReadLmXreturns the pre-read
value(s) for each well at the specified wavelength.
!A1LmXPreRead returns the pre-read value for the
specified well at the indicated wavelength, and
!WellPreReadLmX returns the pre-read values for the
specified wavelength in template order. In CuvetteSet
sections, the !PreRead accessor can be used to display
the REF value.
!CombinedPlot
!WellCombinedPlot
This accessor can be used in Plate or CuvetteSet
sections, for Kinetic runs and Spectrum scans. Returns
the result of the wavelength combination reduction
formula for each well or cuvette (!LmX or !WellLmX
returns information before the wavelength combination
reduction is applied).
!StdDevPlateBlank
Returns the standard deviation value of the plate blank
group.
!StdDevPlateBlankLmX
Specifies the wavelength LmX (e.g., Lm1, Lm2) of the
plate blank group.
!PlateBlankS
!PlateBlankLmXS
!PlateBlankP
!PlateBlankLmXP
56
Returns perpendicular (or S) plate blank raw value(s) for
the given wavelength LmX in a Plate section (e.g., Lm2
or the 2nd wavelength set).
Returns parallel (or P) plate blank raw value(s) for the
given wavelength LmX in a Plate section (e.g., Lm1 or
the 1st wavelength set).
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
4.3. Plate Data Accessors
Example: Dividing All Optical Densities in a Plate Section by the Optical Density in
a Specified Well
You can use a custom formula in the Reduction dialog to divide all optical densities in a
Plate by the optical density in one well:
!Lm1/!A1Lm1
The formula divides the optical density in all wells at wavelength Lm1 (!Lm1) by the
optical density in well A1 (!A1Lm1).
Example: Viewing Optical Densities from Endpoint Reads at Multiple Wavelengths
in a Single Group Section
Several DNA samples were read in a microplate at 260, 280, and 320 nm. PathCheck was
applied to normalize the optical densities to a 1 cm pathlength, and a custom wavelength
reduction formula (!Lm1*50) was entered in the Reduction dialog box of the Plate section
to report the quantitation of the DNA samples.
You can report optical densities at each of the wavelengths in group order with the following formulas:
!WellLm1
!WellLm2
!WellLm3
If these columns are named “OD260”, “OD280” and “OD320” respectively, we can
report a Ratio column to calculate the protein contamination in the DNA samples:
(OD260-OD320)/(OD280-OD320)
Last, we can calculate the average pathlength, in centimeters, for each sample:
Average(!WellPathlength)
Example: Viewing the REF Values for a CuvetteSet
We can calculate a column to show the reference value used for each cuvette using the formula:
!WellPreReadLm1
Creating a column of this kind is quite useful if you have used different reference values
for cuvettes in the same CuvetteSet because it allows you to see the individual reference
values applied to each cuvette and note any differences between them.
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57
4. Accessors
If you have read a CuvetteSet at more than one wavelength, you can see the reference
applied at each wavelength by creating additional columns using modifications of the formula above:
!WellPreReadLm2
!WellPreReadLm3
Example: Viewing the Optical Densities From a Spectrum Scan or Kinetic Run in a
Group Section
When you use !WellLmX to report the optical densities from a Kinetic run or Spectrum
scan in a Group section, the information comes into the table in a horizontal array (the
!TemperatureRun, !WavelengthRun, and !TimeRun accessors also place information in
horizontal arrays). SoftMax Pro allows you to perform further mathematical manipulations on the horizontal array of numbers, but you cannot plot them in a Graph section.
In addition, the display of optical densities from a Kinetic run in the Group section is
affected by whether or not the Absolute Values checkbox in the Reduction dialog is
enabled. When the box is not checked (disabled by default), optical densities are displayed
normalized to 0: the first value for each well is 0.000
When the box is checked (enabled), absolute optical densities are displayed: the first OD
for each well is no longer zero.
If you want to graph the optical densities from a Kinetic run or Spectrum scan, you need
to bring them into the Group section in a columnar format (independent of the template)
instead of a horizontal array (as shown in the example above).
4.4.
PATHCHECK ACCESSORS
PathCheck accessors return information about the values used in the PathCheck calculation as well as information about pathlength. These accessors apply to information in the
Plate section and may be used in Plate sections or in column formulas in Group sections
or in Summary formulas. These accessors are not used in CuvetteSet sections.
Accessor
!Pathlength
!A1Pathlength
Description
Returns the pathlength determined by PathCheck. These
accessors can only be applied to Plate section data.
!Pathlength returns the pathlength for all wells in a plate,
!WellPathlength
!A1Pathlength returns the pathlength for an individual
well, !WellPathlength returns the pathlengths for
samples into a Group section, reporting the information
in template order.
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4.4. PathCheck Accessors
Accessor
!PathCheckLm900
Description
Returns a number representing either the cuvette
reference value read at 900 nm or the value for the
Water Constant at 900 nm, depending on whether the
PathCheck instrument settings are set to use a cuvette
reference or the Water Constant.
!PathCheckLm1000
Returns a number representing either the cuvette
reference value read at 1000 nm or the value for the
Water Constant at 1000 nm, depending on whether the
PathCheck instrument settings are set to use a cuvette
reference or the Water Constant.
!Lm900
!WellLm900
!Lm1000
!WellLm1000
!PathCorrectionOn
Returns (as a list of numbers) the PathCheck values read
from the plate at 900 nm.
Returns (as a list of numbers) the PathCheck values read
from the plate at 1000 nm.
Returns True if the Plate section has been set to use
pathlength correction and False if it has not.
!PathCheckOn
Returns True if PathCheck has been selected in the
Instrument Settings dialog box and returns False if it
has not.
!PathBackground
!PathBackgroundLm1,...!Path
Returns the plate background constant that has been set
for the specified wavelength(s).
BackgroundLm6
Example: Viewing Pathlength together with Pathlength-Corrected Optical Density in
Group Sections
If Pathlength correction is enabled, the !WellValues accessor brings the pathlength-corrected optical density from the Plate section into the Group section.
The formula !WellPathlength reports the pathlength for each well in the group.
Example: Accessing PathCheck Values in a Group Section
The formulas !WellLm900 and !WellLm1000 report the optical density readings from
each well at 900 nm and 1000 nm. These readings are used in the PathCheck calculation
that determines the pathlength in each well.
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59
4. Accessors
You can use the formulas !PathCheckLm900 and !PathCheckLm1000 return the optical
density readings for the cuvette reference at 900 nm and 1000 nm.
If the Water Constant had been used instead of a cuvette reference, these would be the
Water Constant values.
4.5.
GROUP AND WELL INFORMATION ACCESSORS
Group information accessors return information assigned to samples within groups in the
Template Editor. Several of these accessors are the default formulas for the columns that
are created when you create new groups in the Template Editor.
Accessor
!SampleDescriptor
!Concentration
!Factor
Description
Returns the numerical value assigned by the user in the
Sample Descriptor field in the Template Editor, usually
concentration for standards or a dilution factor for
unknowns. The sample descriptor value can be used
with any numerical value you want to associate with a
sample (for example, if it is one of a series of samples
drawn over time, time could be used as a sample
descriptor).
!SampleNames
Returns (as a text string) the sample name assigned in
the Template Editor.
!SampleNumbers
Returns the number of the sample.
!Units
Returns (as a text string) the units assigned to the
sample descriptor in the New Group or Edit Group
dialog box in the Template Editor.
!WellIDs
Returns the well identifier (A1 to H12) for each sample
replicate.
!WellNumbers
Returns the well number of each sample replicate in a
group to the Group section as a list of numbers
(Well A1 = 1…H12 = 96).
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4.6. Blank Accessors
4.6.
BLANK ACCESSORS
Blank accessors allow you to access and manipulate plate blank and group blank information. The average of the plate blank is displayed in the Plate section for Endpoint reads.
The average of the group blank is displayed at the top of each Group section.
Accessor
[email protected]
Description
Returns (as a number) the average of all wells that have
been designated as group blanks for the specified
group.
[email protected]
Returns (as a list of numbers) the values of the
GroupName
individual wells that have been designated as group
blanks for the specified group.
!PlateBlank
Returns the average plate blank value (as a number).
!StdDevPlateBlank
Returns the standard deviation of the plate blank group.
!StdDevPlateBlankLmX
Returns the standard deviation of the plate blank group
at the specified wavelength.
!StdDeviationPlateBlankLm2 returns the standard
deviation of wavelength 2 of the plate blank group.
!PlateBlankS
Returns perpendicular (or S) plate blank raw values for
!PlateBlankSLmXS
the given wavelength LmX in a Plate section.
!PlateBlankLm1S
!PlateBlankP
Returns parallel (or P) plate blank raw values for the
!PlateBlankLmXP
given wavelength LmX in a Plate section.
!PlateBlankLm1P
There is no accessor to access the individual well values of the plate blank as there is for
the group blank. To access these values and get the standard deviation, minimum, maximum, etc., use the specific well accessor (e.g., !A1LmX) in conjunction with a concatenation operator (& or ~) and the appropriate statistical function (Stdev, Min, Max, etc.).
Example: Accessing Group Blank Information
The following formulas can be used in Summaries to report blank group information.
Average group blank:
!GroupBlank
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61
4. Accessors
Standard deviation of the group blank:
Stdev(!GroupBlankValues)
Maximum of group blank values:
Max(!GroupBlankValues)
Minimum of group blank values:
Min(!GroupBlankValues)
Example: Subtracting a Single Plate Blank Value from Multiple Plate Sections
If you want to subtract the same plate blank from multiple groups on different plates, you
can perform the subtraction in the Plate sections.
In this example, the template from first Plate section includes the plate blank. In the second Plate section (containing samples that continue the group from the first Plate section), the reduction formula is set to be the optical density minus the plate blank from
Plate #1. The custom formula for this reduction is:
[email protected]#1
Example: Subtracting a Plate Blank in a Group Section
To subtract a plate blank from a single group that has samples on multiple plates, you
must perform the subtraction in a Group section:
1 Set up the first Plate section and define a plate blank on it.
2 In the Reduction dialog box, disable the Use Plate Blank check box so that the plate
blank is not subtracted automatically from the group. It is very important to do this or
the blank will be subtracted twice from the samples on this plate—once in the Plate
section and again in the Group section.
3 Define the samples belonging to the group in the subsequent Plate sections.
4 Create two custom columns called “Values” and “BlankSbtVal” using the following
formulas respectively:
!WellValues
[email protected]#1
The column named Values reports the reduced numbers from the Plate sections, while
the column named BlankSbtVal subtracts the average OD of the plate blank from each
of the optical densities in the Values column.
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Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
Index
Symbols
!A1LmX 54
!A1LmXPreRead 56
!A1LmXXVals 55
!A1Pathlength 58
!AllValues 56
!AllWavelengths 55
!AutoCutoffOn 46
!AutomixDuration 51
!AutomixOn 51
!AvgReadTemperature 46
!CombinedPlot 56
!Concentration 60
!EmCutoffs 46
!EmFixedWavelength 46
!EmWavelengths 46
!EndLimit 52
!EndSweep 50
!ExFixedOn 46
!ExFixedWavelength 46
!ExWavelengths 47
!Factor 60
!FirstColumn 47
!Gfactor 47
[email protected] 61
[email protected] 61
!IntegrationEnd 47
!IntegrationStart 47
!LastColumn 47
!Lm1000 59
!LmX 54
!MaxLimit 52
!MinLimit 51
!MValue 55
!NumPoints 49
!NumPointsRead 50
!NumWavelengthsRead 50
!NumWells 47
!OnsetOD 52
!OnsetValue 52
!PathBackground 59
!PathBackgroundLm1,...!PathBackgroundLm6 59
!PathCheckLm1000 59
!PathCheckLm900 59
!PathCheckOn 59
!PathCorrectionOn 59
!Pathlength 58
!PlateBlank 61
!PlateBlankLmXP 56
!PlateBlankLmXS 56
!PlateBlankP 56
!PlateBlankS 56
!PlateName 47
!PlateType 47
!PMTSetting 48
!PreMixDuration 48
!PreMixOn 48
!PreReadLmX 56
!PreReadOn 48
!PValue 55
!ReadInterval 50
!ReadsPerWell 48
!ReadType 48
!RunTime 50
!SampleDescriptor 60
!SampleNames 60
!SampleNumbers 60
!StartSweep 50
!StdDevPlateBlank 56
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63
!StdDevPlateBlankLmX 56
!StepSweep 50
!TemperatureRun 51
!TemperatureSetPoint 48
!TimeOfRead 48
!TimeResolvedOn 49
!TimeRun 51
!Units 60
!Values 55
!VMaxPoints 52
!WavelengthRun 51
!Wavelengths 49
!WellAllWavelengths 55
!WellAutoCutoffOn 46
!WellAutomixDuration 51
!WellAutomixOn 51
!WellAvgReadTemperature 46
!WellCombinedPlot 56
!WellEmCutoffs 46
!WellEmFixedWavelength 46
!WellEmWavelengths 46
!WellEndLimit 52
!WellEndSweep 50
!WellExFixedOn 46
!WellExFixedWavelength 46
!WellExWavelengths 47
!WellFirstColumn 47
!WellIDLmXPRaw 55
!WellIDLmXSRaw 55
!WellIDs 60
!WellIntegrationEnd 47
!WellIntegrationStart 47
!WellLastColumn 47
!WellLm1000 59
!WellLm900 59
!WellLmX 54
!WellLmXPRaw 55
!WellLmXSRaw 54
64
!WellLmXXVals 55
!WellMaxLimit 52
!WellMinLimit 51
!WellNumbers 60
!WellNumPointsRead 50
!WellNumwavelengthsRead 50
!WellNumWells 47
!WellOnsetOD 52
!WellOnsetValue 52
!WellPathlength 58
!WellPlateName 47
!WellPlateType 47
!WellPMTSetting 48
!WellPreMixDuration 48
!WellPreMixOn 48
!WellPreReadLmX 56
!WellPreReadOn 48
!WellReadInterval 50
!WellReadsPerWell 48
!WellReadType 48
!WellRunTime 50
!WellStartLimit 52
!WellStartSweep 50
!WellStepSweep 50
!WellTemperatureRun 51
!WellTemperatureSetPoint 48
!WellTimeOfRead 48
!WellTimeResolvedOn 49
!WellTimeRun 51
!WellValues 55
!WellVMaxPoints 52
!WellWavelengthRun 51
!WellWavelengths 49
!XVals 52
& (ampersand) 17
-8
< 10
<= 10
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
Cos 21
Cosh 21
Count 34
CV 24
CVP 24
<> 10
()8
*7
+ 8, 16
/7
=9
>9
>= 10
^8
~ (tilde) 17
D
Delta 34
Division 7
Does Not Equal 10
A
Abs 20
Acos 20
Addition 8
And 11
AntiLog 20
AreaUnder 25
AreaUnderFit 26
Arrays of Numbers 4
ASCII 41
Asin 20
Atan2 20
Average 24
AvgDev 24
B
Blank Accessors 61
C
Case 6
Column Formulas 2
Comparison (Logical) Operators 9
Concat 41
Concatenation Operators 16
Conditional (Boolean) Operators 11
E
Equals 9
Evaluating Column Formulas 6
Exact 41
Exp 21
Exponent 8
F
Fact 21
False 11
FirstArray 34
FirstItem 34
Floor 21
Formula Building Blocks 4
Formula Categories 1
Formula Naming Conventions 4
Formula Size 3
Fract 21
Functions 19
G
Greater Than 9
Greater Than or Equals 10
Group and Well Information Accessors 60
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
65
I
If 11
Index 34
IndexListFor 34
IndexofMax 34
IndexofMin 34
IndexofNearest 35
Int 22
Intercept 27
Interpolation Functions 25
InterpX 27, 28
IsEmpty 40
IsErr 40
Item 35
ItemCount 35
ItemIndex 34
K
Kinetic and Spectrum Data Accessors 49
N
NANs 38
NearestTo 35
Nested Conditionals 12
NoNum 40
Not 11
Now 42
NthArray 35
NthItem 35
NullBetween 35
NullOutside 36
O
L
Left 41
Len 42
Less Than 10
Less Than or Equals 10
Lists of Numbers 4
Ln 22
Log 22
Log10 22
Lower 42
M
MakeErr 40
MakeErrs 38
Mathematical Functions 19
Mathematical Operators 7
66
Max 24
MaxDev 24
Median 24
Mid 42
Min 24
Mod 8
Multiplication 7
Operators 7
Or 11
Ordering Functions in Complex Formulas 5
Other Functions 34
P
Parentheses 8
ParmA 28
ParmB 28
ParmC 28
ParmD 28
PathCheck Accessors 58
Pi 22
Plate Data Accessors 54
Plate/CuvetteSet Setup Information Accessors 46
Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
R
True 11
Rand 22
Reduction Formulas 1
Referencing Columns 6
Referencing Objects in Different Sections 5
RelativePotency 28
Remainder 8
Right 41
Round 22
Rsquared 28
Rules to Follow When Writing Formulas 6
S
Sideways 36
Sign 22
Sin 23
Sinh 23
Slope 28
Special Characters 6
Sqrt 23
Statistical Functions 24
StDev 24
StDevp 24
Strings in Formulas 6
Subtraction 8
Sum 24
Summary Formulas 3
U
Using “Well” as an Accessor Prefix 45
Using Comparison and Conditional Operators 12
Using Mathematical Operators 8
V
Val 42
VMax 31
VMax Reduction Functions 30
VMaxCorr 31
VMaxCorrEx 31
VMaxEx 31
VMaxPerSec 31
VMaxPerSecEx 31
VMaxPtsUsed 32
VMaxPtsUsedEx 32
W
WhatErr 40
T
Tan 23
Tanh 23
Text 42
TimeToVMax 30
TimeToVMaxEx 30
Tips for Writing Conditional Formulas 15
Today 42
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Formula Reference User Guide for SoftMax® Pro Software — 0112-0141 Rev. A
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