I've carried out a GO analysis in R using GOstats, and have a list of p-values. However, as I understand it they have not been corrected for multiple testing, and I cannot see a way to do it in GOstats.
Did I miss something is there a way to do it in GOstats?
I understand why a multiple testing correction may not be appropriate, but all of the web-browser GO programs offer it, and I'd like to see what my results look like with it. I can't seem to find a consensus over whether GO p-values should be corrected or not.
Is there an alternative R package I should use that does offer correction, or is there a way to correct the p-values I have as an output of GOstats?
(I realise there has been many many posts on GO but none have given me exactly what I'm looking for.)
Thanks!
2 answers
If you already have the p-values then you can simply use p.adjust command from the R base package
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/p.adjust.html
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