issues with creating enrichment map

Eva Rosanne Meulendijks

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Mar 5, 2021, 2:13:38 PM3/5/21

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Hello,

Enclosed printscreens from the "creating enrichment map" and the specific error.

I want to do GSEA analysis using the enrichment app in cytoscape, using a preranked file (downloaded from GSEA as well).

After downloading the files from GSEA and using them for the enrichment map, I get the error that none of the genes are found in the expression file.
However, I did not give any expression file as input, so I don't understand what is going wrong.

Could you please help me out?

Much appreciated.

Best,

Eva

Ruth Isserlin

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Mar 5, 2021, 2:31:54 PM3/5/21

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HI Eva,

that error is a little ambiguos. The error means that EM can't match up the gene ids in your rank or expression file to the gene ids in the gmt file. Are the identifiers in your rank file symbols? I can't tell from your screen shots. (GSEA has an option to collapse identifiers, if you are using that option, I am not sure if your rank file would have the old or the new ids)

Thanks,

Ruth

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Ruth Isserlin

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Mar 5, 2021, 2:34:00 PM3/5/21

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also, an aside, if either of those files were opened in Excel they could now have quotes around the gene symbols and EM won't be able to match them up.

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Eva Rosanne Meulendijks

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Mar 9, 2021, 12:31:32 PM3/9/21

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Dear Ruth,

Thank you for the effort answering my question.

By trial and error I found that somehow the preranked file I downloaded from my GSEA enrichment analysis was the issue. I replaced this with my "own" pre ranked file. Using the GSEA file in the first place seems a bit unlogical but I thought filenames needed to match therefore I used this file.