Gene expression annotation files and microarray data formats

The workbench supports analysis of one-color expression arrays. These may be imported from GEO soft sample- or series- file formats, or for Affymetrix arrays, tab-delimited pivot or metrics files, or from Illumina expression files. Expression array data from other platforms may be imported from tab, semi-colon or comma separated files containing the expression feature IDs and levels in a tabular format (see Generic expression and annotation data file formats).

The workbench assumes that expression values are given at the gene level, thus probe-level analysis of e.g. Affymetrix GeneChips and import of Affymetrix CEL and CDF files is currently not supported. However, the workbench allows import of txt files exported from R containing processed Affymetrix CEL-file data (see Affymetrix GeneChip).

Affymetrix NetAffx annotation files for expression GeneChips in csv format and Illumina annotation files can also be imported. Also, you may import your own annotation data in tabular format see Generic expression and annotation data file formats).

Below you find descriptions of the microarray data formats that are supported by Biomedical Genomics Workbench. Note that we for some platforms support both expression data and annotation data.