I would like to do a gene set enrichment analysis using the fgsea tool.
Everything works fine if I use the common Hallmark gene set from WEHI Bioinformatics - mouse and human versions of the MSigDB in R format as a .rdata file.
Now, I would like to use a different (more specific) gene set from GSEA | MSigDB | Browse Mouse Gene Sets. They provide .gmt files that are suitable for the fgsea tool (“A tabular file in GMT file or an RData file containing a list of gene sets, see below for more information”). I adapted the appropiate identifiers in the ranked genes.
Running the tool works without an obvious error message. But the result is basically empty - except the headers.
Has anyone experience or an idea how to solve it?