PTM-SEA error

[aliciar]

Hi everyone, 

I am trying out the Beta version of PTM-SEA (Windows) using the provided data and database and default settings. I am getting the following error message in stderr.txt (Gene Pattern job 42798):

Error in ssGSEA2(input.ds = opt$input.ds, output.prefix = opt$output.prefix,  : 
  object 'm' not found
Execution halted

Any thoughts would be appreciated.

Thanks!

Please respond with the following information as applicable:
 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.

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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: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
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* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

[D R Mani]

Hello,

From the GitHub site at https://github.com/broadinstitute/ssGSEA2.0, using the "Single site-centric phosphoproteome dataset" (PI3K_pert_logP_n2x23936.gct) as "input data" and "PTMsigDB" (ptm.sig.db.all.flanking.human.v1.8.1.gmt) as the "pathway db" should work without any error (see attached screenshot). If some other dataset was being used, please let us know and we can try to debug the issue. 

We are still working on improving error reporting, but the "object 'm' not found" error is an indicator of incorrect input data format.

[Alicia Richards]

Hi,

I am able to get it working with the downloaded data, but get the object 'm' not found when using my dataset (attached).

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[D R Mani]

Hello,

The error was due to incorrect formatting of the input dataset -- the file contains blank columns (see screen shot). An easy way to correctly format gct files is to use Morpheus (https://software.broadinstitute.org/morpheus/). 

The corrected input dataset is attached.