Question regarding ssGSEA

[Jihyun Youn]

Hi,

is there any way to run ssGSEA using RNA expression data that lacks a value for a particular gene for a specific sample? 

Thanks,

Jane

[Anthony Castanza]

Hi Jane,

The general approach is just to fill it in with a zero. But ultimately it depends on why the value is missing.

If it was missing because the software you used did some sort of filtering for non-expressed genes that's probably fine and a 0 is valid. But if was not assayed in the experiment at all but has been added to the list as a result of merging with other samples then just filling it in with a zero is probably not statistically valid, creating separate files for each experiment and quantitating them separately in batch mode with their true assayed gene universe is probably better in this case.

I wish I could give you more concrete advice here, but I just simply don't know enough about how the data was generated and why the value is missing to make a recommendation.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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