Error in rep("null", max.Ng * max.size.G) : invalid 'times' argument

[Catarina Marques]

Hi,

I'm trying to perform ssGSEA imputing my own gene set as a gmt file, but I keep getting the same error message: 

Error in rep("null", max.Ng * max.size.G) : invalid 'times' argument

Calls: ssGSEA.cmdline Execution halted

Could someone help me out? the job nº is 567428. ssGSEA

Thanks a lot!

Catarina

[Anthony Castanza]

Hi Catarina,

It looks like the gene set file you provided was an excel file that was simply renamed to .gmt. In order for ssGSEA to be able to parse the file it needs to be saved out of excel as tab delimited text (.txt), and only then renamed to the .gmt file extension. Once you've corrected the file format your job should run successfully, but let us know if you still encounter errors

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Catarina Marques]

Hi Anthony,

It worked! 

Thank you so much for your help, I really appreciate it!

Cheers,

Catarina

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