probelibraryinfo

Create table of probe set library information

Syntax

ProbeInfo = probelibraryinfo(CELStruct, CDFStruct)


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

Retrieve Probe Set Library Information

This example shows how to extract probe set library information from Affymetrix® GeneChip® microarray data.

This example uses sample data from the E. coli Antisense Genome Array. Download the data from Demo_Data_E-coli-antisense.zip. Extract the data files from the DTT archive using the Data Transfer Tool.

You also need to download Ecoli_ASv2.CDF library file for the E. coli Antisense Genome Array. You may already have these files if you have any Affymetrix GeneChip software installed on your machine. If not, get the library files by downloading and unzipping the E. coli Antisense Genome Array zip file.

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('C:\LibFiles\Ecoli_ASv2.CDF');

Extract probe set library information.

probeInfo = probelibraryinfo(celStruct, cdfStruct);

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

cdfStruct.ProbeSets(probeInfo(1104,1)).Name

ans =

    'thrA_b0002_at'