Enrichment map error when parsing generic results files

[Simon Fox]

I have previously used Enrichment map quite a lot under Cytoscape 3.5. I have just installed latest Cytoscape (3.9.1) and Enrichment Map (3.3.4) for a project. I am loading the generic gem files downloaded from gProfiler analysis and everytime I get the same error message when I try to build a map:"Index 0 out of bound for length 0". This applies even when I try to use input files that have worked fine with earlier versions.

Appreciate some help on what is going on.

Thanks

[Ruth Isserlin]

Hi Simon, 

Sorry about that.  It looks like a bug. I have reported it here - https://github.com/BaderLab/EnrichmentMapApp/issues/489  I will try to figure out a workaround until it gets fixed. 

Thanks, 

Ruth 

On Jun 23, 2022, at 4:25 AM, Simon Fox <simo...@uwa.edu.au> wrote:

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I have previously used Enrichment map quite a lot under Cytoscape 3.5. I have just installed latest Cytoscape (3.9.1) and Enrichment Map (3.3.4) for a project. I am loading the generic gem files downloaded from gProfiler analysis and everytime I get the same error message when I try to build a map:"Index 0 out of bound for length 0". This applies even when I try to use input files that have worked fine with earlier versions.

Appreciate some help on what is going on.

Thanks

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[Simon Fox]

Hi Ruth

Thanks for the reply. I did manage to work around it in the end. I think that the latest versions are less permissive when parsing the formatting of the generic gem files.

I made a few changes so I am not 100% sure exactly which one worked but one thing was previously in the phenotype column I had 1 for upregulation and -1 for down.

When I changed this to +1 and -1 then it seemed to work.

Regards

Simon

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