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I am new to Cytoscape and GSEA, but am trying to build an enrichment map with my RNA-seq data. I have uploaded the .gmt file and two .xls files, one for positive enrichment and one for negative. I also have a .rnk file but that doesn't seem to be causing the issue.

When I select "Build" it gives me the error "Parsing Generic Result file: Index 1 is out of bounds for length 1." Is this referring to one of the my .xls files and how can I adjust the length/formatting to clear this error? The .xls files are just the .tvs files that I got as an output from GSEA and then saved as an .xls.

Thank you for any help.

KBO
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There is no need to convert the tsv files that GSEA is generating to xls files. (In previous versions of GSEA even though it had an xls ending I believe they were just txt files).

Have you tried running Enrichment map with the original tsv files?

Ruth Isserlin
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  • Thank you, it is working now that I have just started using the tsv files. The protocol I was following made it sound like xls files were necessary but that conversion was definitely causing the issue! – KBO Dec 10 '21 at 19:49