Documentation Center

  • Trial Software
  • Product Updates

probesetplot

Plot Affymetrix probe set intensity values

Syntax

probesetplot(CELStruct, CDFStruct, PS)

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

Arguments

CELStructStructure 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.

FieldValueString 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

The following example use a sample CEL file and the CDF library file from the E. coli Antisense Genome array, which you can download from:

http://www.affymetrix.com/support/technical/sample_data/demo_data.affx

After you download the sample data, you will need the Affymetrix Data Transfer Tool to extract the CEL file from a DTT file. You can download the Affymetrix Data Transfer Tool from:

http://www.affymetrix.com/browse/products.jsp?productId=131431&navMode=34000&navAction=jump&aId=productsNav

The following example assumes that the Ecoli-antisense-121502.CEL file is stored on the MATLAB search path or in the current folder. It also assumes that the associated CDF library file, Ecoli_ASv2.CDF, is stored at D:\Affymetrix\LibFiles\Ecoli.

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

    celStruct = affyread('Ecoli-antisense-121502.CEL');
  2. Read the contents of a CDF file into a MATLAB structure.

    cdfStruct = affyread('D:\Affymetrix\LibFiles\Ecoli\Ecoli_ASv2.CDF');
  3. 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)

See Also

| | | |

Was this topic helpful?