Dear all,

please could you advise about the best BioC/R package to use for gene set enrichment analysis ;)

on a side note, may I ask the same question about the easiest package to use for survival analysis :)

many thanks,

-- bogdan

I recommend the GOseq package for GO enrichment analysis, it's quite easy in use if you read the manual first. You only need a list of your significant genes and a list of all your assayed genes.

thank you !

Dear Bogdan,

I'm a bit late for your question but I think the limma package must be mentioned: see the help pages for camera, roast and romer. These are gene set tests, not enrichment tests, i.e., no DEG list required.

Cheers,

 - axel