Error in Running GSEA

[Unsun Lee]

Hi, I'm trying to perform GSEA preranked analysis with my t stat values from limma-voom. I had some trouble loading the data set initially as my rnk file seem to cause parsing errors. I fixed this issue by first saving my excel file as txt, and then changing that txt file into a rnk file. I have followed the rnk file format as specified in https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#RNK:_Ranked_list_file_format_.28.2A.rnk.29. However, now I am experiencing this error when I try to run the GSEAPreranked. Could you help me troubleshoot the problem?

Also, I was wondering is it okay to use the t stat values from my limma-voom TREAT (significance as |logFC|>0.58 and p-val<0.05)? Or is it better to just use the t stat values from my limma-voom without using TREAT?

[David Eby]

Hi,

The error in the screenshot seems to be related to the CHIP chosen for the Collapse operation.  What CHIP have you chosen?

Regarding your question about t stat limma-voom values and TREAT as a ranking metric, we make it a general policy not to offer specific advice on appropriate ranking methods.  GSEAPreranked is generally considered more of an advanced mode for users who want to work with metrics other than those we provide, or whose data is not suitable for those methods.

One of my colleagues can sometimes offer suggestions here, but unfortunately he is away indefinitely and may not be checking messages.

- David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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[Anthony Castanza]

Hi,

With regard to the "t stat values from my limma-voom TREAT (significance as |logFC|>0.58 and p-val<0.05)? Or is it better to just use the t stat values from my limma-voom without using TREAT?" question;
You should use the unfiltered t stat values, where you have a ranking metric for all genes.

Sorry for the delay in getting back to you here, I've been away dealing with a personal matter. Let me know if you have any additional questions

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego