GSEA using different genesets: combined or separate analysis

[A MM]

Dear Anthony,

I would like to ask you a question regarding the analysis of multiple genesets.

We have performed an experiment using mouse ClariomS arrays on RNA mouse brain samples (control and experimental). 

As per your recommendation, we have used:

- Chip file: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Mouse_Clariom_S.r1_Human_Orthologs_MSigDB.v2025.1.Hs_REMAPPED_PATCH.chip

- Geneset: h.all .v2025.1.Hs.symbols.gmt file.

Besides the Hallmark Geneset, we would like to analyze specific genesets obtained form published papers.

My question is: should we perfom he GSEA analysis all at one, using a custom-made file that includes the hallmarks geneset plus additional lines for the genesets obtained from the papers? Or is it better to first do the GSEA analysis with only the Hallmarks geneset and, then, a second analysis with all the specific genesets from the papers or even one specific geneset at a time?

Many thanks in advance for your help,

Amalia

[Anthony Castanza]

Hi Amalia,

My apologies, it seems I missed this message somehow.

Our standard advice is to perform these analyses separately due to the nature of GSEA's competitive test in the FDR calculation.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[A MM]

Thank you so much!

Bes,

AMalia

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