It seems that the multiple test for the GO enrichment result is important. However, the TopGO didn't do that, so I decide to do that by myself. The delemma looks like this: fdr correction with p.adjust() in R need the complete GO enrichment result, whereas the GenTable(,topNodes =N) in TopGO only give out the top N result. So how can I do the "fdr" mutiple test correction to the GO enrichment results from "TopGO"?
Sincerely
•
written
by
dukecomeback •
Instead of specifying topNodes to some value N, you can get all available GO Terms using:
allGO = usedGO(object = GOdata)
# use it in GenTable as follows:
GenTable(GOdata, ... ,topNodes = length(allGO))
Then you can go about doing your p-value adjustment.
•
written
by
komal.rathi
Thank you for all of your help. Finally, the topNodes = length(allGO) from komal.rathi helped me out.
•
written
by
dukecomeback •
Log in to answer this question.
p.adjust only needs a vector of p-values which you can get from the TopGO results. Read the doc: http://www.bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf