Trouble shoot loading rpt file from GSEA in EmrichmentMap App

[Rama Akondy]

Hi, 

-I am a new user using Cytoscape version 3.6.1 on windows 8. 

-When I open the EnrichmenMap app and try and load an rpt file generated in GSEA (so all the relevant files are populated) , I get a message saying "Cytoscape does not recognize files with the suffix .rpt" (screenshot attached). I understand it is possible to load individual files but this looks simpler (if it works). Please help.

Thanks

Rama

[Ruth Isserlin]

Hi Rama, 

Yes.  If you are used to the original way it worked then it is confusing.  In the latest version the ability to specify the rpt directly was removed.  It still has the functionality though. 

To get the same functionality instead of clicking the "+" to create an new enrichment map click on the folder icon.  Navigate to the gsea result directory and select it (don't go into the directory but just select the directory) and then click "open".  EM with automatically find the rpt file and populate all the fields.

Thanks, 

Ruth 

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[Rama Akondy]

Hi Ruth, Thank you for the prompt response. I tried loading the folder and some things were populated (the gct, cls files) but not the GMT or the positive or negative enrichments. When I hit 'build' I got an error message saying "enrichment files OR GMT file are needed". When I loaded the GMT file (not from the results folder but one I had dowloaded from the MSIgDB website), the build button was greyed out.

I did load the files manually and wan able to run the analysis (very few networks though) , so i will continie to load files manually,

Just one question - the GMT file used should be the one containing all the genesets from the MsigDB website, correct?

Regards

Rama

[Ruth Isserlin]

Hi Rama, 

That is very weird behaviour.  It should have loaded the gmt and enrichment results.  Did you by any chance move the GSEA directory after GSEA created it or change the names of any of the files?  (that shouldn't effect how the loading is working though)  Can you send me GSEa results folder so I can try and figure out what is going on? 

With regards to what GMT file to use, it depends on which GMT file you have used to run the analysis. In the gsea interface you would have selected with msigdb file to use.  You should use whichever one you selected.  GSEA with put a filtered copy of the gmt file you used in the results directory in the edb directory but it is better to use the original gmt file that can be download from the MSigdb website ( http://software.broadinstitute.org/gsea/downloads.jsp)

Thanks, 

Ruth 

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[Rama Akondy]

Hi Ruth,

1. No, I did not change the default location and neither did I change any of the file names.

2. Please let me know the best way to share the results folder with you.

Best
Rama

On Thursday, October 11, 2018 at 11:04:36 AM UTC-4, risserlin wrote:

Hi Rama, 

That is very weird behaviour.  It should have loaded the gmt and enrichment results.  Did you by any chance move the GSEA directory after GSEA created it or change the names of any of the files?  (that shouldn't effect how the loading is working though)  Can you send me GSEa results folder so I can try and figure out what is going on? 

With regards to what GMT file to use, it depends on which GMT file you have used to run the analysis. In the gsea interface you would have selected with msigdb file to use.  You should use whichever one you selected.  GSEA with put a filtered copy of the gmt file you used in the results directory in the edb directory but it is better to use the original gmt file that can be download from the MSigdb website ( http://software.broadinstitute.org/gsea/downloads.jsp)

Thanks, 

Ruth 

On Wed, Oct 10, 2018 at 5:29 PM Rama Akondy <rama.a...@gmail.com> wrote:

Hi Ruth, Thank you for the prompt response. I tried loading the folder and some things were populated (the gct, cls files) but not the GMT or the positive or negative enrichments. When I hit 'build' I got an error message saying "enrichment files OR GMT file are needed". When I loaded the GMT file (not from the results folder but one I had dowloaded from the MSIgDB website), the build button was greyed out.

I did load the files manually and wan able to run the analysis (very few networks though) , so i will continie to load files manually,

Just one question - the GMT file used should be the one containing all the genesets from the MsigDB website, correct?

Regards

Rama

On Wednesday, October 10, 2018 at 3:18:32 PM UTC-4, Rama Akondy wrote:

Hi, 

-I am a new user using Cytoscape version 3.6.1 on windows 8. 

-When I open the EnrichmenMap app and try and load an rpt file generated in GSEA (so all the relevant files are populated) , I get a message saying "Cytoscape does not recognize files with the suffix .rpt" (screenshot attached). I understand it is possible to load individual files but this looks simpler (if it works). Please help.

Thanks

Rama

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