Only one get set in results file

[Clotilde Thumser]

Hey,

I was rerunning some samples in the software with an expression dataset and labels that I already used a few months ago to do the exact same analysis. The first time (a few months ago) gave a few gene sets that were differentially expressed. Now when I rerun this analysis, only one gene set appears in the result file, and all the others gene sets show a "rejected" status.  (in the same analysis that I ran a few months ago, none of the gene sets were shown as rejected). Do you know any reason that could caue this problem ?

Thank you very much !

Best regards,

Clotilde Thumser-Henner

[Anthony Castanza]

Hi Clotilde,

 

The “Rejected” status is given when, after looking at the intersection of the gene names in the input expression list and the gene set the intersection is smaller than the minimum size threshold in GSEA.

 

The most likely cause I could think of is that, if you previously ran your experiment with a different version of MSigDB, and your new run uses the current version of MSigDB, but you didn’t reconvert your gene identifiers, either using the CHIP files for the current MSigDB version or otherwise. This could cause GSEA to be unable to recognize what had been previously matching genes. Another possibility is the opposite, where if you took gene sets from an old version of MSigDB, but are using one of the new chip files targeting the current 7.2 version. That would cause the same mismatch issue.

 

I would recommend carefully double checking your input files to ensure that you’re using the correct CHIP file for both your input dataset, and the version of MSigDB that your gene sets were taken from.

 

Let me know if you’re still having issues after validating these inputs.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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