What array platforms and organism species does GSEA support?
GSEA works on any data, as long as the gene identifiers in your expression data (the GCT file) match those in the gene sets (the GMT file), or if you have a CHIP file that provides the mapping between gene identifiers in your expression data and gene identifiers in the gene sets. All gene sets in MSigDB use human gene symbols regardless of the original organism. Consequently, our CHIP files provide the mappings from different platforms (e.g., mouse Affymetrix probe set IDs, human Affymetrix probe set IDs, etc.) to human gene symbols. To see what platforms (CHIP files) are available: start GSEA desktop application and click […] at “Chip platform(s)” on “Run GSEA” page. If your platform is not in this list, you have the following options: • Create your own CHIP file to map your platform specific gene identifiers to human gene symbols and then use your CHIP file to collapse dataset in GSEA. The CHIP file format is described here: CHIP file format.
Related Questions
- Can I hybridize samples to an array from a species other than the organism for which the array was designed? For example, can I hybridize a mouse sample to a rat chip?
- Does this mean that GenArts will be de-emphasizing support for other host platforms?
- What platforms and devices do NAVTEQ’s LBA services support?
