For performing a gene enrichment analysis, we used the following settings for the R-function runGSA (piano package);
gsaRes_xxx<-runGSA(pval_xxx, geneSetStat="fisher", directions=fc_xxx, signifMethod="nullDist", adjMethod="BH", gsc=gsc, gsSizeLim=c(5,Inf))
fc_xxx = log2fc of genes (ouput deseq2)
pval_xxx = the p-values (output deseq2) or should we use the adj p-value from deseq2?
This seemed to work, can anyone confirm our settings?