For expression data, use the GCT file format. This a tab-delimited format that contains a row for each probe set ID (or gene), a column for each sample, and expression values for each feature in each sample.
To display expression data, IGV must first map the probe set IDs named in the expression data file to their genomic locations. IGV displays data for all of the probes that it can map to genomic locations. If none of the probes in the file can be mapped, IGV displays an error message.
IGV determines the genomic locations for probes as follows:
Choose preferred mapping: By default, IGV uses its probe mapping files before its gene mapping files. If you prefer to map probes to genes, select the Map probes to genes radio button on the Probes tab of the Preferences window.
Probe mapping files map probe identifiers to chromosomal locations. They are compiled from source files provided by Affymetrix, Agilent, and Illumina. The Affymetrix and Agilent mapping files are split by species due to their large size. Separate mapping files are provided for human, mouse, and other (non-mouse, non-human) species. Human probe identifiers are mapped to hg18. Depending on the vendor, mouse probe identifiers are mapped to mm9 (Affymetrix), mm5 (Agilent) or mm8 (Illumina).
Following are links to the probe mapping files:
Gene mapping files map probe identifiers to gene identifiers. Following are links to the gene mapping files:
Sources for the Mapping Files
The probe and gene mapping files are compiled from source files provided by Affymetrix, Agilent, and Illumina. A list of the source files is available at http://www.broadinstitute.org/igv/resources/probes/data_sources_for_mapping.txt.