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probesetplot

Plot Affymetrix probe set intensity values

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Syntax

probesetplot(CELStruct, CDFStruct, PS)
probesetplot(CELStruct, CDFStruct, PS, ...'GeneName', GeneNameValue, ...)
probesetplot(CELStruct, CDFStruct, PS, ...'Field', FieldValue, ...)
probesetplot(CELStruct, CDFStruct, PS, ...'ShowStats', ShowStatsValue, ...)

Arguments

CELStruct Structure created by the affyread function from an Affymetrix® CEL file.
CDFStructStructure created by the affyread function from an Affymetrix CDF library file associated with the CEL file.
PSProbe set index or the probe set ID/name.
GeneNameValueControls whether the probe set name or the gene name is used for the title of the plot. Choices are true or false (default).

Note

The 'GeneName' property requires the GIN library file associated with the CEL and CDF files to be located in the same folder as the CDF library file from which CDFStruct was created.

FieldValueCharacter vector or string specifying the type of data to plot. Choices are:

  • 'Intensity' (default)

  • 'StdDev'

  • 'Background'

  • 'Pixels'

  • 'Outlier'

ShowStatsValueControls whether the mean and standard deviation lines are included in the plot. Choices are true or false (default).

Description

probesetplot(CELStruct, CDFStruct, PS) plots the PM (perfect match) and MM (mismatch) intensity values for a specified probe set. CELStruct is a structure created by the affyread function from an Affymetrix CEL file. CDFStruct is a structure created by the affyread function from an Affymetrix CDF library file associated with the CEL file. PS is the probe set index or the probe set ID/name.

Note

MATLAB® software uses 1-based indexing for probe set numbers, while the Affymetrix CDF file uses 0-based indexing for probe set numbers. For example, CDFStruct.ProbeSets(1) has a ProbeSetNumber of 0 in the ProbePairs field.

probesetplot(CELStruct, CDFStruct, PS, ...'PropertyName', PropertyValue, ...) calls probesetplot with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

probesetplot(CELStruct, CDFStruct, PS, ...'GeneName', GeneNameValue, ...) controls whether the probe set name or the gene name is used for the title of the plot. Choices are true or false (default).

Note

The 'GeneName' property requires the GIN library file associated with the CEL and CDF files to be located in the same folder as the CDF library file from which CDFStruct was created.

probesetplot(CELStruct, CDFStruct, PS, ...'Field', FieldValue, ...) specifies the type of data to plot. Choices are:

  • 'Intensity' (default)

  • 'StdDev'

  • 'Background'

  • 'Pixels'

  • 'Outlier'

probesetplot(CELStruct, CDFStruct, PS, ...'ShowStats', ShowStatsValue, ...) controls whether the mean and standard deviation lines are included in the plot. Choices are true or false (default).

Examples

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Open Script

You need some sample data files from here. This example uses the sample data from the E. coli Antisense Genome Array. Extract the data files from the DTT archive using the Data Transfer Tool.

You also need to download the corresponding library files for the sample. For this example, Ecoli_ASv2.CDF and Ecoli_ASv2.GIN are used as for the E. coli Antisense Genome Array. You may already have these files if you have any Affymetrix GeneChip software installed on your machine. If not, get the library files by downloading the E. coli Antisense Genome Array zip file from here.

Read the contents of a CEL file into a MATLAB structure.

celStruct = affyread('Ecoli-antisense-121502.CEL');

Read the contents of a CDF file into a MATLAB structure.

cdfStruct = affyread('C:\LibFiles\Ecoli_ASv2.CDF');

Plot the PM and MM intensity values of the argG_b3172_at probe set, including the mean and standard deviation.

probesetplot(celStruct, cdfStruct, 'argG_b3172_at','showstats', true)

Version History

Introduced before R2006a

See Also

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