I'm trying to perform GSEA with the fgsea package in R:
However, I receive the error:
Warning message: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (5.02% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results.
As suggested by this post: https://github.com/YuLab-SMU/clusterProfiler/issues/214, I have randomly ranked values with the same log2fc. However, I still receive the same error. I had also removed genes with NA values for log2fc (I don't know if this is necessary). However, I still receive the same error. Has anybody encountered this issue and knows how to solve it?
My stats object looks something like this:
My pathways object looks something like this:
Also, when I try to see if the rank is duplicated:
The result is FALSE. So I'm really unsure of why I receive this warning