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probelibraryinfo

Create table of probe set library information

Syntax

ProbeInfo = probelibraryinfo(CELStruct, CDFStruct)

Input 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.

Output Arguments

ProbeInfoThree-column matrix with the same number of rows as the Probes field of the CELStruct.
  • Column 1 — Probe set ID/name to which the probe belongs. (Probes that do not belong to a probe set in the CDF library file have probe set ID/name equal to 0.)

  • Column 2 — Contains the probe pair number.

  • Column 3 — Indicates if the probe is a perfect match (1) or mismatch (-1) probe.

Description

ProbeInfo = probelibraryinfo(CELStruct, CDFStruct) creates a table of information linking the probe data from CELStruct, a structure created from an Affymetrix CEL file, with probe set information from CDFStruct, a structure created from an Affymetrix CDF file.

    Note:   Affymetrix probe pair indexing is 0-based, while MATLAB® software indexing is 1-based. The output from probelibraryinfo is 1-based.

Examples

The following example uses 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. Extract probe set library information.

    ProbeInfo = probelibraryinfo(celStruct, cdfStruct);
  4. Determine the probe set to which the 1104th probe belongs.

    cdfStruct.ProbeSets(ProbeInfo(1104,1)).Name
    
    ans =
    
    thrA_b0002_at

See Also

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