ssGSEA - Error with uploading gct file format

[Deena Maurer]

Hello, 

I am a new user to GenePattern and I am trying to run ssGSEA analysis. I followed the format online, but an error occurs when attempting to run the analysis: "Error in read.dataset(input.ds) : Input is not a res or gct file.

Calls: ssGSEA.cmdline Execution halted"

Job ID: ssGSEA (509444)

My input file has a ".gct.txt" extension, which I am assuming might be the problem, but I am unsure how to get rid of the ".txt" portion. This file is able to run on the GSEA platform, so I am unsure of why the error persists here. Any help is appreciated! 

[Anthony Castanza]

Hi Deena, 

Yes the txt file extension is the problem here. The standard GSEA software is written to handle this extra extension but unfortunately that protection is not present in the ssGSEA implementation on GenePattern.

In order to show and remove this extra file extension you'll need to enable your operating system's option to "show hidden file extensions". If you're unable to locate this option, let me know what operating system you're using and I should be able to help direct you. 

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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[Deena Maurer]

Thanks, Anthony! That is helpful. Will proceed with removing the txt file extension.