Error ssGSEA(595651)

[Kudzayi Kutywayo]

Hello, I have been trying to run ssGSEA but it keeps coming up with an error message (with no explanation). I have tried changing the job memory allocation but I'm getting the same result. Would you be able to help me with this please?

[John Liefeld]

Hi,  please provide a job number for us to look at,

Thanks

Ted

[John Liefeld]

I made the assumption that your username was khkutty (seems close to your email).  So if Job 595674 is one of yours, the proximal answer is in the stderr.txt file that the job output.

"No output gct file written: no gene sets satisfied the min overlap criterion"

I will forward this to one of the GSEA developers to see if they have advice for how to  address "no gene sets satisfying the min overlap criterion". 

Hope this helps

Ted

[Anthony Castanza]

Hi Kudzayi,

It looks like your dataset is using Ensembl Gene IDs as the input gene identifier. Since MSigDB gene sets are provided in Gene Symbols (or NCBI gene IDs), n order to run ssGSEA on this data with MSigDB gene sets you first need to run your dataset through the "CollapseDataset" module: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00134:2.2.0

You'll want to select the "Human_Ensembl_Gene_ID_MSigDB.v.2023.2.Hs.chip" file for this combination of gene IDs and gene sets.

Let us know if you have any more questions

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Kudzayi Kutywayo]

Thank you very much! I was able to run ssGsea after collapsing the dataset.