trying to run ssGSEAProjection can't get gct formatted correctly

[dl...@foghorntx.com]

Hello

I'm trying to run sGSEAProjection and I believe I'm having a problem with the GCT I'm using for my input.gct.file parameter.  I'm running on the public, Broad-hosted GenePattern server, the job ID is 1711290.

The error message I'm receiving (stderr.txt) is:

Error in read.gct(file) : 
  Number of sample names 1 not equal to the number of columns 2 .Number of sample names 1 not equal to the number of columns 0 .
Calls: ssGSEA.projection.cmdline
Execution halted

Here's the top of my gct file, produced with the cmapPy python library:

#1.3
1000	2	0	0
id	col2	col1
a000	834.0000	223.0000 

a001 622.0000 729.0000

I don't know where the code is getting the "sample names" from (and that there is only 1 of them).  I would have guessed it would be using the gct dimensions and/or the column headers for the matrix in the gct file, but that is not the case. 

Any help much appreciated!

Thanks,

Dave

[Edwin Juarez]

Hello Dave,

It seems like cmapPy is creating version 1.3 of the GCT file format. You'd need to use version 1.2 of the format as described here: http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#GCT

As for your question about where the code is getting the number of sample names, note that GCT version 1.2 requires a "Name" and a "Description" columns, so my guess is that ssGSEA is seeing 3 total columns and guesses that there is only one "data column" (based on the assumption that the GCT file is version 1.2).

Edwin.

[dl...@foghorntx.com]

Thank you Edwin - that did it!  I reformatted to GCT 1.2 and it worked fine.