Building Enrichment Map error

[TarekGharsalli]

Hello,

Does any one encoutered this error when building Enrichment map:

Index 1 out of bounds for length 1

Thanks,

[TarekGharsalli]

[mikekucera]

Please make sure you are using the latest version of the EnrichmentMap app.

[gharsallitarek]

Thanks @mikekucera for your reply. My EnrichmentMap version is 3.3.5, and I saw that the new version is 3.5

[TarekGharsalli]

Hi @mikekucera ,

I installed the latest version of cytoscape and enrichmentMap, but I get another error: could not parse line 3 of enrichment file. here the example of file that I tested from gprofiler Test_enrichment_Map.txt

Thanks for your help !

[risserlin]

The file you uploaded is not the right file type.
I think you might have downloaded the csv file instead of the GEM file. You need to make sure to download the GEM file if you want to use your gprofiler results with EM

[gharsallitarek]

thanks @risserlin for your reply and help. There is any way to adapt my file ? I used gProfiler on R and I did analysis based on the pathways that I found. If I will use the pprofiler on browser, I need to repeat all the analysis that I did. Thanks !

[risserlin]

Here is a link to an R code example of running g:profiler from R and how I transform the results I get back to the right format for EM - https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/run-gprofiler-from-r.html

specifically section 4.6 but you need the g:profiler gmt file as well - https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/run-gprofiler-from-r.html#create-an-output-file-of-the-results---generic-enrichment-map-file-from-gprofiler-gmt

[gharsallitarek]

Thanks a lot ! @risserlin