Where is it possible to find gene sets in rdata format for GSEA ?
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Aurora ▴ 20
@aurora-15104
Last seen 6.1 years ago

I would like to perform GSEA in R using the camera method from limma. However I work on Rattus Norvegicus data and I don't find any Rdata file available to use as a gene set. I only foud this website : http://bioinf.wehi.edu.au/software/MSigDB/mouse_c2_v5p1.rdata but gene sets are only available for mouse and human.

Thank you

Gsea rattus norvegicus • 1.6k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

No where. The MSigDb itself maintained by the Broad Institute is deliberately only for human. We made a mouse version for our own purposes at the WEHI. If you want a Rattus version of MSigDb you would have to make it yourself.

Rattus versions of GO, KEGG or Reactome exist however.

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