probelibraryinfo - Create table of probe set library information

Syntax

Input Arguments

CELStruct	Structure created by the affyread function from an Affymetrix CEL file.
CDFStruct	Structure created by the affyread function from an Affymetrix CDF library file associated with the CEL file.

Output Arguments

ProbeInfo

Three-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 demo 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

affyread | celintensityread | probesetlink | probesetlookup | probesetplot | probesetvalues

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