Tied Ranks in fgsea
Entering edit mode
zli1 • 0
Last seen 1 day ago
United States

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?

fgsea • 130 views
Entering edit mode

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 DESeq2 analysis.


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