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

`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.
`PS`	Probe 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

`PSValues`	Twenty-column matrix with one row for each probe pair in the probe set.
`ColumnNames`	Cell array of character vectors 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.

Column	Field	Description
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 character vectors 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

collapse all

Retrieve Affymetrix™ Probe Set Intensity Values

Open Script

For this example, you need some sample data files from here. This example uses the sample data from the E. coli Antisense Genome Array. Extract the data files from the DTT archive using the Data Transfer Tool.

You also need to download the corresponding library files for the sample. For this example, Ecoli_ASv2.CDF and Ecoli_ASv2.GIN are used as 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 the E. coli Antisense Genome Array zip file from here.

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');

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);

Create a table of intensity values for the argG_b3172_at probe set.

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

psvals =

   1.0e+03 *

  Columns 1 through 7

    5.2120         0         0    0.0454    0.4300    0.1770    0.1690
    5.2120    0.0010         0    0.0455    0.4310    0.1770    0.1273
    5.2120    0.0020         0    0.0455    0.4320    0.1770    0.1270
    5.2120    0.0030         0    0.0455    0.4330    0.1770    0.1333
    5.2120    0.0040         0    0.0455    0.4340    0.1770    0.2123
    5.2120    0.0050         0    0.0455    0.4350    0.1770    0.1495
    5.2120    0.0060         0    0.0455    0.4360    0.1770    0.0503
    5.2120    0.0070         0    0.0456    0.4370    0.1770    0.1525
    5.2120    0.0080         0    0.0456    0.4380    0.1770    0.1645
    5.2120    0.0090         0    0.0456    0.4390    0.1770    0.1260
    5.2120    0.0100         0    0.0456    0.4400    0.1770    0.0540
    5.2120    0.0110         0    0.0456    0.4410    0.1770    0.0833
    5.2120    0.0120         0    0.0457    0.4420    0.1770    0.0955
    5.2120    0.0130         0    0.0457    0.4430    0.1770    0.1100
    5.2120    0.0140         0    0.0457    0.4440    0.1770    0.2510

  Columns 8 through 14

    0.0354    0.0250         0         0    0.4300    0.1780    0.1635
    0.0218    0.0300         0         0    0.4310    0.1780    0.1003
    0.0237    0.0300         0         0    0.4320    0.1780    0.1750
    0.0259    0.0360         0         0    0.4330    0.1780    0.0940
    0.0433    0.0360         0         0    0.4340    0.1780    0.1718
    0.0275    0.0360         0         0    0.4350    0.1780    0.1540
    0.0112    0.0300         0         0    0.4360    0.1780    0.0460
    0.0377    0.0360         0         0    0.4370    0.1780    0.1070
    0.0312    0.0360         0         0    0.4380    0.1780    0.0973
    0.0234    0.0360         0         0    0.4390    0.1780    0.1213
    0.0112    0.0360         0         0    0.4400    0.1780    0.0540
    0.0174    0.0360         0         0    0.4410    0.1780    0.0623
    0.0171    0.0300         0         0    0.4420    0.1780    0.0840
    0.0196    0.0360         0         0    0.4430    0.1780    0.0925
    0.0460    0.0360         0         0    0.4440    0.1780    0.1118

  Columns 15 through 20

    0.0241    0.0300         0         0    0.0010    0.0020
    0.0146    0.0360         0         0    0.0010    0.0020
    0.0286    0.0360         0         0    0.0010    0.0020
    0.0227    0.0300         0         0    0.0010    0.0020
    0.0365    0.0300         0         0    0.0010    0.0020
    0.0303    0.0300         0         0    0.0010    0.0020
    0.0098    0.0250         0         0    0.0010    0.0020
    0.0210    0.0360         0         0    0.0010    0.0020
    0.0219    0.0360         0         0    0.0010    0.0020
    0.0253    0.0360         0         0    0.0010    0.0020
    0.0129    0.0360         0         0    0.0010    0.0020
    0.0125    0.0360         0         0    0.0010    0.0020
    0.0186    0.0300         0         0    0.0010    0.0020
    0.0220    0.0360         0         0    0.0010    0.0020
    0.0207    0.0360         0         0    0.0010    0.0020

Version History

Introduced before R2006a