Bioinformatics Toolbox

probesetvalues

Extract probe set values from probe results

Syntax

PSValues = probesetvalues(CELStruct, CDFStruct, PS)

Description

PSValues = probesetvalues(CELStruct, CDFStruct, PS) creates a table of values for a probe set (PS) from the probe data in a CEL file structure (CELStruct). PS is a probe set index or probe set name from the CDF library file structure (CDFStruct). PSValues is a matrix with 18 columns and one row for each probe pair in the probe set. The columns correspond to the fields in a CHP probe set data structure:

 'ProbeSetNumber'
      'ProbePairNumber'
      'UseProbePair'
      'Background'
      'PMPosX'
      'PMPosY'
      'PMIntensity'
      'PMStdDev'
      'PMPixels'
      'PMOutlier'
      'PMMasked'
      'MMPosX'
      'MMPosY'
      'MMIntensity'
      'MMStdDev'
      'MMPixels'
      'MMOutlier'
      'MMMasked'

There are some minor differences between the output of this function and the data in a CHP file. The PM and MM Intensity values in the CHP file are normalized by the Affymetrix software. This function returns the raw intensity values. The 'UseProbePair' and 'Background' fields are only returned by this function for compatibility with the CHP probe set data structure and are always set to zero.

Examples

celStruct = affyread('Drosophila-121502.cel');
cdfStruct = affyread('D:\Affymetrix\LibFiles\DrosGenome1\...
                      DrosGenome1.CDF');
% get the values for probe set 147439_at
psvals = probesetvalues(celStruct,cdfStruct,'147439_at')

probesetvalues

Syntax

Description

Examples

See Also