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probesetvalues

Create table of Affymetrix probe set intensity values

Syntax

PSValues = probesetvalues(CELStruct, CDFStruct, PS)
PSValues = probesetvalues(CELStruct, CDFStruct, PS, 'Background', BackgroundValue)
ColumnNames = probesetvalues

Input Arguments

CELStructStructure created by the affyread function from an Affymetrix® CEL file.
CDFStructStructure created by the affyread function from an Affymetrix CDF library file associated with the CEL file.
PSProbe set index or the probe set ID/name.
BackgroundValue

Controls the background correction in the calculation. Choices are:

  • true (default) — Background values from the Background field in the PSValues matrix are used to calculate the probe intensity values.

  • false — Background values are not calculated.

  • A vector of precalculated background values (such as returned by the zonebackadj function) whose length is equal to the number of probes in CELStruct. These background values are used to calculate the probe intensity values.

    Tip   Including background correction in the calculation of the probe intensity values can be slow. Therefore, setting 'Background' to false can speed up the calculation. However, the values returned in the 'Background' field of the PSValues matrix will be zero.

Output Arguments

PSValuesTwenty-column matrix with one row for each probe pair in the probe set.
ColumnNamesCell array of strings containing the column names of the PSValues matrix. This is returned only when you call probesetvalues with no input arguments.

Description

PSValues = probesetvalues(CELStruct, CDFStruct, PS) creates a table of intensity values for PS, a probe set, from the probe-level data in CELStruct, 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. PSValues is a twenty-column matrix with one row for each probe pair in the probe set. The columns correspond to the following fields.

ColumnFieldDescription
1'ProbeSetNumber'Number identifying the probe set to which the probe pair belongs.
2'ProbePairNumber'Index of the probe pair within the probe set.
3'UseProbePair'This field is for backward compatibility only and is not currently used.
4'Background'Estimated background of probe intensity values of the probe pair.
5'PMPosX'x-coordinate of the perfect match probe.
6'PMPosY'y-coordinate of the perfect match probe.
7'PMIntensity'Intensity value of the perfect match probe.
8'PMStdDev'Standard deviation of intensity value of the perfect match probe.
9'PMPixels'Number of pixels in the cell containing the perfect match probe.
10'PMOutlier'True/false flag indicating if the perfect match probe was marked as an outlier.
11'PMMasked'True/false flag indicating if the perfect match probe was masked.
12'MMPosX'x-coordinate of the mismatch probe.
13'MMPosY'y-coordinate of the mismatch probe.
14'MMIntensity'Intensity value of the mismatch probe.
15'MMStdDev'Standard deviation of intensity value of the mismatch probe.
16'MMPixels'Number of pixels in the cell containing the mismatch probe.
17'MMOutlier'True/false flag indicating if the mismatch probe was marked as an outlier.
18'MMMasked'True/false flag indicating if the mismatch probe was masked.
19'GroupNumber'Number identifying the group to which the probe pair belongs. For expression arrays, this is always 1. For genotyping arrays, this is typically 1 (allele A, sense), 2 (allele B, sense), 3 (allele A, antisense), or 4 (allele B, antisense).
20'Direction'Number identifying the direction of the probe pair. 1 = sense and 2 = antisense.

    Note:   MATLAB® software uses 1-based indexing for probe set numbers, while the Affymetrix CDF file uses 0-based indexing for probe set numbers. For example, CDFStruct.ProbeSets(1) has a ProbeSetNumber of 0 in the ProbePairs field.

PSValues = probesetvalues(CELStruct, CDFStruct, PS, 'Background', BackgroundValue) controls the background correction in the calculation. BackgroundValue can be:

  • true (default) — Background values from the Background field in the PSValues matrix are used to calculate the probe intensity values.

  • false — Background values are not calculated.

  • A vector of precalculated background values (such as returned by the zonebackadj function) whose length is equal to the number of probes in CELStruct. These background values are used to calculate the probe intensity values.

    Tip   Including background correction in the calculation of the probe intensity values can be slow. Therefore, setting 'Background' to false can speed up the calculation. However, the values returned in the 'Background' field of the PSValues matrix will be zero.

ColumnNames = probesetvalues returns a cell array of strings containing the column names of the PSValues matrix. ColumnNames is returned only when you call probesetvalues without input arguments. The information contained in ColumnNames is common to all Affymetrix GeneChip® arrays.

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 sample 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/browse/products.jsp?productId=131431&navMode=34000&navAction=jump&aId=productsNav

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

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

    celStruct = affyread('Ecoli-antisense-121502.CEL');
  2. Read the contents of a CDF file into a MATLAB structure.

    cdfStruct = affyread('D:\Affymetrix\LibFiles\Ecoli\Ecoli_ASv2.CDF');
  3. Use the zonebackadj function to return a matrix or cell array of vectors containing the estimated background values for each probe.

    [baData,zones,background] = zonebackadj(celStruct,'cdf',cdfStruct);
  4. Create a table of intensity values for the argG_b3172_at probe set.

    psvals = probesetvalues(celStruct, cdfStruct, 'argG_b3172_at',...
             'background',background);

See Also

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