Entering edit mode
Hello all,
I was trying to perform GSEA for a dataset using the fgsea R package. The code I used was
fgseaRes <- fgsea(pathways = pathways,
stats = ranks,
minSize = 5,
maxSize = Inf)
I received an warning saying that
There are ties in the preranked stats (73.72% of the list)
It was my first time doing GSEA and according to a vignette (https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/RNASeq2018/html/06_Gene_set_testing.nb.html) it's said as long as the number of tied ranks is low it should be okay, but the number 73.72% looks unsettling to me.
I obtained the log fold-change using DESeq2. Is there anything I could do to fix the problem?
The message strongly suggests that the vast majority of the genes in your list have exactly the same value/ranking (i.e. log2FC). This would worry me very much. I would start by double-checking that you indeed extracted the correct information from the results of the
DESeq2analysis.