Bioinformatics Toolbox™

celintensityread - Read probe intensities from Affymetrix CEL files

Syntax

ProbeStructure = celintensityread(CELFiles, CDFFile) ProbeStructure = celintensityread(..., 'CELPath', CELPathValue, ...) ProbeStructure = celintensityread(..., 'CDFPath', CDFPathValue, ...) ProbeStructure = celintensityread(..., 'PMOnly', PMOnlyValue, ...) ProbeStructure = celintensityread(..., 'Verbose', VerboseValue, ...)

Arguments

`CELFiles`	Any of the following: String specifying a single CEL file name. `''`, which reads all CEL files in the current directory. `' '`, which opens the Select CEL Files dialog box from which you select the CEL files. From this dialog box, you can press and hold Ctrl* or Shift while clicking to select multiple CEL files. Cell array of CEL file names.
`CDFFile`	Either of the following: String specifying a CDF file name. `' '`, which opens the Select CDF File dialog box from which you select the CDF file.
`CELPathValue`	String specifying the path and directory where the files specified in `CELFiles` are stored.
`CDFPathValue`	String specifying the path and directory where the file specified in `CDFFile` is stored.
`PMOnlyValue`	Property to include or exclude the mismatch (MM) probe intensity values in the returned structure. Enter `true` to return only perfect match (PM) probe intensities. Enter `false` to return both PM and MM probe intensities. Default is `true`.
`VerboseValue`	Controls the display of a progress report showing the name of each CEL file as it is read. When `VerboseValue` is `false`, no progress report is displayed. Default is `true`.

Return Values

ProbeStructure MATLAB structure containing information from the CEL files, including probe intensities, probe indices, and probe set IDs.

Description

Note This function does not work on the Solaris platform.

ProbeStructure = celintensityread(CELFiles, CDFFile) reads the specified Affymetrix CEL files and the associated CDF library file (created from Affymetrix GeneChip arrays for expression or genotyping assays), and then creates ProbeStructure, a structure containing information from the CEL files, including probe intensities, probe indices, and probe set IDs. CELFiles is a string or cell array of CEL file names. CDFFile is a string specifying a CDF file name.

If you set CELFiles to '*', then it reads all CEL files in the current directory. If you set CELFiles to ' ', then it opens the Select CEL Files dialog box from which you select the CEL files. From this dialog box, you can press and hold Ctrl or Shift while clicking to select multiple CEL files.

If you set CDFFile to ' ', then it opens the Select CDF File dialog box from which you select the CDF file.

ProbeStructure = celintensityread(..., 'PropertyName', PropertyValue, ...) calls celintensityread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

ProbeStructure = celintensityread(..., 'CELPath', CELPathValue, ...) specifies a path and directory where the files specified by CELFiles are stored.

ProbeStructure = celintensityread(..., 'CDFPath', CDFPathValue, ...) specifies a path and directory where the file specified by CDFFile is stored.

ProbeStructure = celintensityread(..., 'PMOnly', PMOnlyValue, ...) includes or excludes the mismatch (MM) probe intensity values. When PMOnlyValue is true, celintensityread returns only perfect match (PM) probe intensities. When PMOnlyValue is false, celintensityread returns both PM and MM probe intensities. Default is true.

You can learn more about the Affymetrix CEL files and download sample files from:

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

Note Some Affymetrix CEL files are combined with other data files in a DTT or CAB file. You must download and use the Affymetrix Data Transfer Tool to extract these files from the DTT or CAB file. You can download the Affymetrix Data Transfer Tool from:

http://www.affymetrix.com/products/software/specific/dtt.affx

You will have to register and log in at the Affymetrix Web site to download the Affymetrix Data Transfer Tool.

ProbeStructure contains the following fields.

Field	Description
`CDFName`	File name of the Affymetrix CDF library file.
`CELNames`	Cell array of names of the Affymetrix CEL files.
`NumChips`	Number of CEL files read into the structure.
`NumProbeSets`	Number of probe sets in each CEL file.
`NumProbes`	Number of probes in each CEL file.
`ProbeSetIDs`	Cell array of the probe set IDs from the Affymetrix CDF library file.
`ProbeIndices`	Column vector containing probe indexing information. Probes within a probe set are numbered `0` through `N - 1`, where `N` is the number of probes in the probe set.
`GroupNumbers`	Column vector containing group numbers for probes within the probe set. For gene expression data, the group number for all probes is `1`. For SNP (genotyping) data, the group numbers for probes are: `1` — Allele A – (sense) `2` — Allele B – (sense) `3` — Allele A + (antisense) `4` — Allele B + (antisense)
`PMIntensities`	Matrix containing perfect match (PM) probe intensity values. Each row corresponds to a probe, and each column corresponds to a CEL file. The rows are ordered the same way as in `ProbeIndices`, and the columns are ordered the same way as in the `CELFiles` input argument.
`MMIntensities` (optional)	Matrix containing mismatch (MM) probe intensity values. Each row corresponds to a probe, and each column corresponds to a CEL file. The rows are ordered the same way as in `ProbeIndices`, and the columns are ordered the same way as in the `CELFiles` input argument.

ProbeStructure = celintensityread(..., 'Verbose', VerboseValue, ...) controls the display of a progress report showing the name of each CEL file as it is read. When VerboseValue is false, no progress report is displayed. Default is true.

Examples

The following example assumes that you have the HG_U95Av2.CDF library file stored at D:\Affymetrix\LibFiles\HGGenome, and that your current directory points to a location containing CEL files associated with this CDF library file. In this example, the celintensityread function reads all the CEL files in the current directory and a CDF file in a specified directory. The next command line uses the rmabackadj function to perform background adjustment on the PM probe intensities in the PMIntensities field of PMProbeStructure.

PMProbeStructure = celintensityread('*', 'HG_U95Av2.CDF',...
	                  'CDFPath', 'D:\Affymetrix\LibFiles\HGGenome');
BackAdjustedMatrix = rmabackadj(PMProbeStructure.PMIntensities);

The following example lets you select CEL files and a CDF file to read using Open File dialog boxes: