Problem with building enrichment map

[Ermir Zulfaj]

Hello!

This error pops up when trying to build my enrichment map:  "parsing generic result file, white/red minus sign For input string: "I<". 

I am a new user of cytoscape and I´m facing this challenge when trying to create an enrichment map from my GSEA results (reactome pathways).

I am uploading the positively and negatively enriched pathways (.xls files; ID column containing the reactome id, description column, size column, ES column, NES, NOM p-val, FDR q-val, FWER p-val, RANK AT MAX, LEADING EDGE), and the .gmt file for the Reactome pathways (downladed from baderlab: http://download.baderlab.org/EM_Genesets/current_release/Rat/UniProt/Pathways/Rat_Reactome_March_01_2024_UniProt.gmt). 

Data set edges is automatic with middle connectivity, 0,05 FDR. 

Both cytoscape and enrichment map was recently downloaded and should be up to date. 

kindest,

[jingj...@gmail.com]

Hi Ermir, 

could you provide an example xls file here, or to Ruth in the other post so that we can reproduce the error?

Thanks,

Jing

[Ruth Isserlin]

Hi Jing, 

Ermir sent the files to me privately.  The issue has been resolved.  It was a formatting issue with the underlying files.  

Thanks, 

Ruth 

On Mar 14, 2024, at 2:59 AM, jingj...@gmail.com <jingj...@gmail.com> wrote:

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[Ruth Isserlin]

Oops.  I thought this was a previous post but it looks new.  Disregard my previous email.

On Mar 14, 2024, at 2:59 AM, jingj...@gmail.com <jingj...@gmail.com> wrote:

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[Ruth Isserlin]

Hi Ermir,

Please send me an example file that is not working if the below suggestion doesn’t work. EM  isn’t recognizing your enrichment file as coming from GSEA because the error message says it is trying to parse a generic file as opposed to a GSEA results file.  The GSEA file should contain 11 columns as follows:

name

description

GS details

SIZE

ES

NES

pval

padj

FWER

Rank at Max

leading edge genes

From your list of columns it looks like you only have 10 and are missing the column GS details.  

Thanks, 

Ruth 

On Mar 7, 2024, at 10:49 AM, Ermir Zulfaj <ermir....@gmail.com> wrote:

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