Bioinformatics Toolbox™

probelibraryinfo - Create table of probe set library information

Syntax

ProbeInfo = probelibraryinfo(CELStruct, CDFStruct)

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.

Return Values

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/products/software/specific/dtt.affx

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

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

Extract probe set library information.

ProbeInfo = probelibraryinfo(celStruct, cdfStruct);

Determine the probe set to which the 1104th probe belongs.