GSEAPreranked with customized gene set

[Anna Huang]

Has anyone had experience in running GSEAPreranked with a customized gene set? I constructed a gene set in .gmt file as attached. After I ran the GSEAPreranked, it gave me Error (1001) and the error message (attached) saying the "After pruning, none of the gene sets passed size thresholds."
 

My gene set has 307 genes, so it's within the limit of 15 - 500 per GSEA User Guide. And now I don't know what the problem might come from. I ran the GSEA with the GSEA software.

If someone could share some experience and insight that would be much appreciated. Thanks in advance! 

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[Anthony Castanza]

Hi Anna,

A gene set passing the thresholds or not is both a function of the gene set size and how many of those genes are present in the dataset being tested. Essentially, the threshold is only applied after the gene set is filtered to the experimental gene universe.

This message would imply that fewer than 15 genes of the set were actually present in your ranked list. However, this can also be caused by a namespace mismatch. In your gmt file, the data appears to be mouse-convention formatted gene symbols. Does your dataset match this, and/or are you using our mapping CHIP files to translate your data into this namespace?

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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