Bioinformatics Toolbox™

probesetlookup - Look up information for Affymetrix^® probe set

Syntax

PSStruct = probesetlookup(AffyStruct, ID)

Arguments

`AffyStruct`	Structure created by the `affyread` function from an Affymetrix CHP file or an Affymetrix CDF library file for expression assays.
`ID`	Probe set ID/name or gene ID.

Return Values

PSStruct

Structure containing the following fields for a probe set:

Identifier — Gene ID associated with the probe set
ProbeSetName — Probe set ID/name
CDFIndex — Index into the CDF structure for the probe set
GINIndex — Index into the GIN structure for the probe set
Description — Description of the probe set
Source — Source(s) of the probe set
SourceURL — Source URL(s) for the probe set

Description

PSStruct = probesetlookup(AffyStruct, ID) returns a structure containing information for an Affymetrix probe set specified by ID, a probe set ID/name or gene ID, and by AffyStruct, a structure created from an Affymetrix CHP file or Affymetrix CDF library file for expression assays.

Note This function works with CHP files and CDF files for expression assays only. It requires that the GIN library file associated with the CHP file or CDF file to be located in the same directory as the CDF library file.

Examples

The following example uses 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

The following example assumes that the Ecoli_ASv2.CDF library file is stored at D:\Affymetrix\LibFiles\Ecoli.

Read the contents of a CDF library file into a MATLAB^® structure.

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

Look up the gene ID (Identifier) associated with the argG_b3172_at probe set.

probesetlookup(cdfStruct,'argG_b3172_at')

ans = 

      Identifier: '3315278'
    ProbeSetName: 'argG_b3172_at'
        CDFIndex: 5213
        GINIndex: 3074
     Description: [1x82 char]
          Source: 'NCBI EColi Genome'
       SourceURL: [1x74 char]