Affymetrix GeneChip

For Affymetrix, three types of files are currently supported: Affymetrix .CHP files, Affymetrix NetAffx annotation files and tab-delimited pivot or metrics files. Affymetrix .CEL files are currently not supported. However, the Bioconductor R package 'affy' allows you to preprocess the .CEL files and export a txt file containing a table of estimated probe-level expression values in three lines of code:

library(affy) # loading Bioconductor library 'affy'
data=ReadAffy() # probe-level data import
eset=rma(data) # probe-level data pre-processing using 'rma'
write.exprs(eset,file="evals.txt") # writing probe expression levels to 'evals-txt'

The exported txt file (evals.txt) can be imported into the workbench using the Generic expression data table format importer (Generic expression and annotation data file formats; you can just 'drag-and-drop' it in). In R, you should have all the CEL files you wish to process in your working directory and the file 'evals.txt' will be written to that directory.

If multiple probes are present for the same gene, further processing may be required to merge them into a single gene-level expression.

Affymetrix CHP expression files

The Affymetrix scanner software produces a number of files when a GeneChip is scanned. Two of these are the .CHP and the .CEL files. These are binary files with native Affymetrix formats. The Affymetrix GeneChips contain a number of probes for each gene (typically between 22 and 40). The .CEL file contains the probe-level intensities, and the .CHP file contains the gene-level information. The gene-level information has been obtained by the scanner software through postprocessing and summarization of the probe-level intensities.

In order to interpret the probe-level information in the .CEL file, the .CDF file for the type of GeneChip that was used is required. Similarly for the .CHP file: in order to interpret the gene-level information in the .CHP file, the .PSI file for the type of GeneChip that was used is required.

In order to import a .CHP file it is required that the corresponding .PSI file is present in the same folder as the .CHP file you want to import, and furthermore, this must be the only .PSI file that is present there. There are no requirements for the name of the .PSI file. Note that the .PSI file itself will not be imported - it is only used to guide the import of the .CHP file which contains the expression values.

Download example .CHP and .PSI files here (note that these are binary files):

Affymetrix metrix files

The Affymetrix metrics or pivot files are tab-delimited files that may be exported from the Affymetrix scanner software. The metrics files have a lot of technical information that is only partly used in the Workbench. The feature ids (Probe Set Name), expression values (Used Signal), absent/present call (Detection) and absent/present p-value (Detection p-value) are imported into the Workbench.

Download a small example sample file here:

Affymetrix NetAffx annotation files

The NetAffx annotation files for Whole-Transcript Expression Gene arrays and 3' IVT Expression Analysis Arrays can be imported and used to annotate experiments as shown in Adding annotations.

Download a small example annotation file here which includes header information: