The cls.file must be categorical with exactly two classes Execution halted

[Komal Rathi]

Please respond with the following information as applicable:
 A complete description of the problem (ie what you were trying to do and what went wrong):

I am trying to normalize my gene matrix using DESeq2 to be used for downstream GSEA anlaysis. I have 8 classes defined, but I thought that is permissible for GSEA analysis?

This is the error:

Error in GP.deseq2(gct, cls, confounding.var.cls, opts$qc.plot.format,  : 
  The cls.file must be categorical with exactly two classes
Execution halted

Job ID if run on a publicly available server.

237567

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right-hand corner of the module input page or here: https://www.genepattern.org/modules
* GenePattern FAQ - https://www.genepattern.org/FAQ
* GenePattern  Videos - https://www.genepattern.org/video-tutorials
* GenePattern File Formats - https://www.genepattern.org/file-formats-guide#file-formats
* GenePattern User Guide - https://www.genepattern.org/user-guide#user-guide
* GenePattern Programmer's Guide - https://www.genepattern.org/programmers-guide
* GenePattern Release Notes - https://github.com/genepattern/genepattern-server/releases/latest

Please respond with the following information as applicable:
 A complete description of the problem (ie what you were trying to do and what went wrong):

Job ID if run on a publicly available server.

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right-hand corner of the module input page or here: https://www.genepattern.org/modules
* GenePattern FAQ - https://www.genepattern.org/FAQ
* GenePattern  Videos - https://www.genepattern.org/video-tutorials
* GenePattern File Formats - https://www.genepattern.org/file-formats-guide#file-formats
* GenePattern User Guide - https://www.genepattern.org/user-guide#user-guide
* GenePattern Programmer's Guide - https://www.genepattern.org/programmers-guide
* GenePattern Release Notes - https://github.com/genepattern/genepattern-server/releases/latest

[Anthony Castanza]

Hello,

Our implementation of DESeq2 on GenePattern is unfortunately limited to two defined phenotype classes in the CLS file. This is due to the primary use of this module being for differential expression analysis and limitation in how classes are selected for that procedure through the GenePattern UI.

DESeq2 can normalize datasets with additional classes but it would have to be done manually using DESeq2's R package in a local environment.

-Anthony

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

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