Good afternoon,
I was wondering if someone could advise me on the following:
I am running FGSEA with my DESEQ2 results in Hallmarks following below code:
# Prepare results from DESEQ2
res<- res[order(-res$stat),]
ranks<-res$stat
names(ranks)<-res$hgnc_symbol
# Run gene set enrichment analysis
fgseaRes <- fgsea(pathways=pathways.hallmark, stats=ranks,nperm=10000)
However, my pathway results change signficantly if I change the number of permutations (e.g. from 1000 to 10000). I am not quite sure which number of permutations I should choose?
Thank you!
You can find your answer in a previous post here: nperm value in GSEA setting
the smallest p-value for 1000 permutation is 1/1000 and if you increase it to 10000, the smallest p-value you can get is 1/10000