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

**URL:** <https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099>\
**Category:** Uncategorized\
**Tags:** transcriptomics, rna-seq\
**Created:** [November 6, 2023, 11:01am UTC](https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099 "2023-11-06T11:01:34Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Sebastian](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sebastian](https://help.galaxyproject.org/u/Sebastian)\
**Post date:** [November 6, 2023, 11:01am UTC](https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099/1 "2023-11-06T11:01:34Z")

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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](https://bioinf.wehi.edu.au/software/MSigDB/index.html) as a .rdata file.

Now, I would like to use a different (more specific) gene set from [GSEA | MSigDB | Browse Mouse Gene Sets](https://www.gsea-msigdb.org/gsea/msigdb/mouse/genesets.jsp?collection=CP:WIKIPATHWAYS). 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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<div class="post-metadata">

**Author:** ![Sebastian](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@Sebastian](https://help.galaxyproject.org/u/Sebastian)\
**Post date:** [November 6, 2023, 1:22pm UTC](https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099/2 "2023-11-06T13:22:18Z")

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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