Help with ssGSEA

[Patricia Muskus]

Hello, 

I am obtaining the following error when attempting to run the ssGSEA module: 

Error in `[.data.frame`(column.names, 3:length(column.names)) : undefined columns selected Calls: ssGSEA.cmdline Execution halted

602548. ssGSEA

Thanks in advance!

[Anthony Castanza]

Hi Patricia,

The gct file you used appears to be, internally, an xml file. This is typically caused by renaming an .xlsx file produced by excel to gct directly. In order to create a properly formatted GCT file it first must be saved out of excel as tab delimited text (.txt) and only then can it be renamed to .gct.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Patricia Muskus]

Thanks Anthony, ssGSEA worked!

I'm now trying to visualize the results using the ConstellationMap module. To do this, I first created a cls file with ClsFileCreator.  However, when I pass both the .gct and .cls file onto ConstellationMap, I get the following error: 

Error in MSIG.ReadPhenFile.2(file = cls.filename) : Failed to parse input cls file cls.cls. Expected 3 lines in categorical type CLS file. Instead saw 6 lines.

Execution halted  

602571. ConstellationMap

Thanks again,

Patricia

[Anthony Castanza]

Hi  Patricia,

I'm not sure why it thinks there are 6 lines in the CLS, it's possible that it's choking on the / character in the phenotype names. Additionally, spaces in phenotype names for cls files aren't supported.

Try using the attached CLS file instead, I did some cleanup to bring the phenotype names in line with the format expectations.

That said, I've never run a dataset with more than two phenotypes through Constellation map so I'm not entirely sure if it's supported.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/0bf6c5b1-1d66-447e-a4d9-71439952b00an%40googlegroups.com.

[Patricia Muskus]

Thanks Anthony, I went ahead and narrowed it down to two groups. 

I'm sorry for all the questions, I'm still very new at this. I'm now encountering the following problem:

Warning message: In readLines(file) : incomplete final line found on '/opt/gpcloud/gp_home/users/guest_98824/uploads/tmp/run5851885708483540510.tmp/input.cls.file/2/count_cleaned%20%28selected%20grouops%29.PROJ%20%281%29.cls' Error: Failed to match all gene set names from count_cleaned (selected grouops).PROJ (1).gct with corresponding gene sets from h.all.v2024.1.Hs.symbols.gmt Be sure that the gene set file matches the original from the upstream job, including version, and that combine.off is used with ssGSEAProjection if applicable. Execution halted