Unsuccessful run

[Pratibha Garg]

I uploaded the pre ranked file (log2FC) and a GMT file with both the upregulated and downregulated proteins in the dataset. Every time I run, it shows error and shows duplicate gene sets in data.

[Anthony Castanza]

Hello,

Are you using the current release of MSigDB - v7.5.1? There was an error in the preparation of v7.5 that resulted in a duplicate set which caused us to release the corrected 7.5.1 version.

Another possible cause of this error could be selecting both a parent collection, and one of its children - such as both c2.all.v7.5.1 and c2.cp.reactome.v7.5.1

If you're providing our own gene sets and not ones you've retrieved from MSigDB/the built-in options, I'd suggest opening the gmx/gmt files in a plain text editor and ensuring that none of the set names are duplicated.

If it isn't any of these issues, sending a screenshot of your Run GSEAPreranked window might help us in determining what could be going wrong here.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

On Tue, May 17, 2022 at 4:28 AM Pratibha Garg <pgarg...@gmail.com> wrote:

I uploaded the pre ranked file (log2FC) and a GMT file with both the upregulated and downregulated proteins in the dataset. Every time I run, it shows error and shows duplicate gene sets in data.

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