There are several packages that implement functions for a Gene Set (Enrichment) Analysis, some of them are limma, gsar, gsva, piano, fgsea, pgsea. However I couldn't find an agreement for those tests which accept any statistic as input:
Using plotting functions, like
barcodeplot, I found that the results can change based on which statistics I use. If I use limma's topTable result as input I have the logFC, t, B P.value, adj.P.value and AveExpr statistics. Are there any recommendations or articles to read about which one is better?
Of course doing the analysis with P.value and adj.P.value will result on similar results but there are noticeable differences when I use logFC or t values.