ssGSEA error

[vineelaga...@gmail.com]

Hi ,

I am getting the following error. Jobid  451521

Error in `[<-`(`*tmp*`, start:(start + N.gs - 1), 1:max(GSDB$size.G), : subscript out of bounds Calls: ssGSEA.cmdline Execution halted

Is this a memory issue. Could you please help me debug this.

Thanks!

[Anthony Castanza]

Hello,

So at least part of the issue here is that ssGSEA has an internally hard-coded maximum gene set size. Gene Sets over 2000 members are automatically rejected. This is causing the ACHILLES_COMMON_ESSENTIALS set to be thrown away by the parser. However, I am not entirely sure why it isn't continuing on to quantify the second set which appears to be within expected limits, it is possible our parser has a small glitch if the first set is thrown away leaving only one set in the data (this is an edge case that may have escaped our testing). You might try submitting this second set individually, but to get the first set to work you'll need to find some way to refine it to be a more specific marker of the desired process.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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