Permutations FGSEA

Question

[Bine]

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!

[bk11]

You can find your answer in a previous post here: nperm value in GSEA setting

[Ming Tommy Tang]

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

Answer 1

[alserg]

You don't really need to specify nperm anymore (it even produces a warning if you do so). It's only supported for backward compatibility purposes and it results in using an older and less efficient algorithm.