Trouble with GSEA data import

[Siegmund Lang]

Hello everyone!

I´m using cytoscape v.3.2.0 for the first time and I´m confronted with a very basic problem:

I want to visualize my GSEA data in a enrichment map with cytoscape. Therefore I got the EnrichmentMap App, selected the GSEA Analyis Type and used the GSEA output .rpt file for Expression in Dataset 1. All other needed data files were added automatically by the program, so I assumed the were chosen in the right format etc..
But after hitting the "Build" butten the program reports this error: "None of the genes in the rank file are found in the expression file. Make sure the identifiers of the two files match."

Any ideas?
Thank you very much for your help!

[Ruth]

Hi, 

Are you doing your Gsea analysis with probe level expression ( with the collapse probes option in the Gsea interface). If so you will need to generate a different gct file using the collapsedataset tool in Gsea. 

Ruth

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[Siegmund Lang]

Hi,

thank you for your answer!
I´m using "Collapse data set to gene symbols" = false.

[Siegmund Lang]

Hi, thank you for your answer!

i´m using "collapse data set to gene symbols" = false.

Am Sonntag, 11. Januar 2015 18:09:56 UTC+1 schrieb risserlin:

Hi, 

Are you doing your Gsea analysis with probe level expression ( with the collapse probes option in the Gsea interface). If so you will need to generate a different gct file using the collapsedataset tool in Gsea. 

Ruth

On Jan 11, 2015, at 10:35 AM, Siegmund Lang <lang.s...@gmail.com> wrote:

Hello everyone!

I´m using cytoscape v.3.2.0 for the first time and I´m confronted with a very basic problem:

I want to visualize my GSEA data in a enrichment map with cytoscape. Therefore I got the EnrichmentMap App, selected the GSEA Analyis Type and used the GSEA output .rpt file for Expression in Dataset 1. All other needed data files were added automatically by the program, so I assumed the were chosen in the right format etc..
But after hitting the "Build" butten the program reports this error: "None of the genes in the rank file are found in the expression file. Make sure the identifiers of the two files match."

Any ideas?
Thank you very much for your help!

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[Lisa Bedford]

Hello,

I am having the same issue as Siegmund Lang. I have looked at both of the files and the genes are present. Can someone please help?

Thanks,

Lisa

[Ruth]

Hi Lisa,

Which files have you checked for the matching genes?

Thanks,

Ruth

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Lisa Bedford
Sent: April-11-16 4:12 PM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] Trouble with GSEA data import

 

Hello,

 

I am having the same issue as Siegmund Lang. I have looked at both of the files and the genes are present. Can someone please help?

 

Thanks,

Lisa

On Saturday, January 17, 2015 at 8:27:32 AM UTC-5, Siegmund Lang wrote:

Hi, thank you for your answer!
i´m using "collapse data set to gene symbols" = false.

Am Sonntag, 11. Januar 2015 18:09:56 UTC+1 schrieb risserlin:

Hi, 

Are you doing your Gsea analysis with probe level expression ( with the collapse probes option in the Gsea interface). If so you will need to generate a different gct file using the collapsedataset tool in Gsea. 

 

Ruth

On Jan 11, 2015, at 10:35 AM, Siegmund Lang <lang.s...@gmail.com> wrote:

Hello everyone!

I´m using cytoscape v.3.2.0 for the first time and I´m confronted with a very basic problem:

I want to visualize my GSEA data in a enrichment map with cytoscape. Therefore I got the EnrichmentMap App, selected the GSEA Analyis Type and used the GSEA output .rpt file for Expression in Dataset 1. All other needed data files were added automatically by the program, so I assumed the were chosen in the right format etc..
But after hitting the "Build" butten the program reports this error: "None of the genes in the rank file are found in the expression file. Make sure the identifiers of the two files match."

Any ideas?
Thank you very much for your help!

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