GSEA ghost files on Windows

[Kevin Lee]

When using particular gene sets database; in my case it was a baderlab.gmt (Human_GOBP_AllPathways_no_GO_iea_March_01_2021_symbol.gmt) for performing a GSEAPreranked analysis. The software saves any files of enrichment results regardless of the gene set name given by the selected database, problem arises when the gene set name contains a colon ":" (ex. "ExampleGeneSet%GOBP%GO:xxxxxx.tsv"). This is an apparent problem on Windows for which I could not explain in technical detail, chromium browsers and certain R functions on Windows are able to access these files. But when physically navigating and accessing through Windows' file explorer; or running R code accessing these files(ex. loading generated .tsv) through docker, the file will, and cannot be found. Not sure if this is intended.

Running GSEA 4.2.3 GUI Java, W10

Thanks, Kev

[David Eby]

Hi Kevin,

Yes, you are correct.  I wouldn't say it's "intended" behavior, but GSEA Desktop is rather sensitive to any kind of special character, particularly those that might have meaning to the operating system or in a web browser context, for example.  We've corrected for this in places but it's a fairly old code base and it's somewhat difficult to track down all the cases.

Our standard advice is to stick with alphanumeric only for gene set names, file names, etc, with underscores in place of any such special characters.  We'll keep working on improving this in future releases, but the above advice is safest in general.  It's not a great situation, since gene set names have meaning to whoever created them and so renaming them in any way can obscure that meaning.  However, *not* renaming them can lead to these kinds of access & display issues.

Thanks,

David

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

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