affysnpquartets

Create table of SNP probe quartet results for Affymetrix probe set

Syntax

SNPQStruct = affysnpquartets(CELStruct, CDFStruct, PS)

Input Arguments

CELStructStructure created by the affyread function from an Affymetrix® CEL file, which contains information about the intensity values of the individual probes.
CDFStructStructure 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.
PSProbe set index or the probe set ID/name.

Output Arguments

SNPQStructStructure 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.

FieldDescription
'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 folder. It also assumes that the associated CDF library file, Mapping50K_Hind240.cdf, is stored at D:\Affymetrix\LibFiles\.

  1. Read the contents of a CEL file into a MATLAB structure.

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

    cdfStruct = affyread('D:\Affymetrix\LibFiles\Mapping50K_Hind240.cdf');
  3. 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]
  4. View the intensity values of the first probe pair in the probe set.

    SNPQStruct.Quartet(1)
    
    ans = 
    
            A_Sense_PM: 5013
            B_Sense_PM: 1290
            A_Sense_MM: 1485
            B_Sense_MM: 686
        A_Antisense_PM: 3746
        B_Antisense_PM: 1406
        A_Antisense_MM: 1527
        B_Antisense_MM: 958
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