fgsea of gene sets in .gmt does not provide any output

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Hello everyone,

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?

Best regards,
Sebastian

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Update:
I solved the problem.
Uploading and using the .gmt file was not the problem.

For this specific but confined gene set, I simply set the “Minimum size of gene set” too high.

Thanks for anyone who put some thoughts into it.

Best regards,
Sebastian

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