generating GSEA analysis from a particular dataset

[Priyanka Manandhar]

Hi Anthony, 

Is it possible, using the GSEA software to generate analysis using a single targeted dataset that I have identified and downloaded as opposed to all the comparisons that the software does by default?

Thanks, 

Priya 

[Anthony Castanza]

Hi Priya,

 

I'm not entirely sure what you mean by a "single targeted dataset" do you mean a single gene set?
In wich case, the answer is yes, but the FDR won't be a meaningful statistic, so you'll want to base your evaluation of the enrichment score on just the NOM P-value.

If you mean just a single sample of expression data, that's a little more complicated of an answer but we do have separate tools for that (ssGSEA on GenePattern in particular).

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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