difficulties running ssGSEA

[Vijay Putatunda]

hello,

I am trying to run ssGSEA, but am encountering the following error:

Error in vector(length = gene.set.size, mode = "character") : invalid 'length' argument Calls: ssGSEA.cmdline Execution halted

I know my gct file works because I was able to run the GSEA hallmark gene set. I am not sure what is wrong with my gmt file (attached). Could you please advise?

thank you,

Vijay

[Castanza, Anthony]

Hi Vijay,

The issue might be with the quotes and commas in the gene set names in your file, I’d recommend removing those and trying again

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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