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Question: Where is it possible to find gene sets in rdata format for GSEA ?
0
gravatar for Aurora
10 months ago by
Aurora10
Aurora10 wrote:

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

rattus norvegicus gsea • 219 views
ADD COMMENTlink modified 10 months ago by Gordon Smyth36k • written 10 months ago by Aurora10
Answer: Where is it possible to find gene sets in rdata format for GSEA ?
1
gravatar for Gordon Smyth
10 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Gordon Smyth36k
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