Bioinformatics Toolbox™

affysnpquartets - Create table of SNP probe quartet results for Affymetrix probe set

Syntax

SNPQStruct = affysnpquartets(CELStruct, CDFStruct, PS)

Arguments

`CELStruct`	Structure created by the `affyread` function from an Affymetrix CEL file, which contains information about the intensity values of the individual probes.
`CDFStruct`	Structure created by the `affyread` function from an Affymetrix CDF library file associated with the CEL file. The CDF library file contains information about which probes belong to which probe set.
`PS`	Probe set index or the probe set ID/name.

Return Values

SNPQStruct Structure containing probe quartet results for a specific SNP probe set from the data in a CEL file and associated CDF library file.

Description

SNPQStruct = affysnpquartets(CELStruct, CDFStruct, PS) creates SNPQStruct, a structure containing probe quartet results for a specific SNP probe set, specified by PS, from the probe-level data in a CEL file and associated CDF library file. CELStruct is a structure created by the affyread function from an Affymetrix CEL file. PS is a probe set index or probe set ID/name from CDFStruct, a structure created by the affyread function from an Affymetrix CDF library file associated with the CEL file. SNPQStruct is a structure containing the following fields.

Field	Description
`'ProbeSet'`	Identifier for the probe set.
`'AlleleA'`	String specifying the base that is allele A for the probe set.
`'AlleleB'`	String specifying the base that is allele B for the probe set.
`'Quartet'`	Structure array containing intensity values for PM (perfect match) and MM (mismatch) probe pairs, including the sense and antisense probes for alleles A and B. Each structure in the array corresponds to a probe pair in the probe set.

Examples

The following example uses the NA06985_Hind_B5_3005533.CEL file. You can download this and other sample CEL files from:

http://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx

The NA06985_Hind_B5_3005533.CEL file is included in the 100K_trios.hind.1.zip file.

The following example uses the CDF library file for the Mapping 50K Hind 240 array, which you can download from:

http://www.affymetrix.com/support/technical/byproduct.affx?product=100k

The following example assumes that the NA06985_Hind_B5_3005533.CEL file is stored on the MATLAB search path or in the current directory. It also assumes that the associated CDF library file, Mapping50K_Hind240.cdf, is stored at D:\Affymetrix\LibFiles\.

Read the contents of a CEL file into a MATLAB structure.
```
celStruct = affyread('NA06985_Hind_B5_3005533.CEL');
```

Read the contents of a CDF file into a MATLAB structure.

cdfStruct = affyread('D:\Affymetrix\LibFiles\Mapping50K_Hind240.cdf');

Create a structure containing SNP probe quartet results for the SNP_A-1684395 probe set.

SNPQStruct = affysnpquartets(celStruct,cdfStruct,'SNP_A-1684395')

SNPQStruct = 

    ProbeSet: 'SNP_A-1684395'
     AlleleA: 'A'
     AlleleB: 'G'
     Quartet: [1x5 struct]

View the intensity values of the first probe pair in the probe set.