RNAseq rnk file return "A 'chip.platform.file' must be provided for collapse/remap" Error

[Domenico Somma]

Hi, I am using GSEAPreranked with a .rnk file I generated from RNAseq data, with HUGO gene names. The same file works with v6.0.12 but doesn't with v7.0.3, and the error says:

"2071 [ERROR ] - A 'chip.platform.file' must be provided for collapse/remap

2091 [ERROR ] - Error while processng:

2091 [ERROR ] - There were one or more errors with the job parameters.

Please check log output for details."

If there is a mistake in the rnk file I generated, I don't understand the older version of the software is working, but not the new one.

JobID not working, v7.0.3: 189965
JobID working, v6.0.12: 189843

Thanks

Best Regards

[Anthony Castanza]

Hi,

To align with changes that we implemented in GSEA Desktop Preranked, version 7 of the module allows the GSEA collapse dataset function. The default value of this collapse dataset parameter expects that you provide a chip file in order to process your gene identifiers using the Remap Only mode. This allows us to make sure that the version of Gene Symbols used in the input ranked list are consistent with the symbols used in MSigDB.

If you do not wish to provide a chip file, make sure the "collapse dataset" parameter is set to "No collapse"

This should resolve the error that you are seeing.

-Anthony

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

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