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broadinstitute / ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
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Small test.gct file works fine but whole data.gct gives incorrect number of dimensions error #20

Closed qianxu05172019 closed 3 years ago

qianxu05172019 commented 3 years ago

Hi,

I have one gene count sample and was using the online ssGSEA tool here: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00270:10.0.4

I prepared my own.gct file and tried to do a ssGSEA experiment. When I upload the whole data.gct to the platform and usingc1.all.v7.2.symbols.gmt as geneset files. Using the default settings, it keeps giving an "incorrect number of dimensions" error. But when I extract part of the file by hand as a test.gct file, it just works fine.

I have attached both my count.gct and test.gct here. Can you please help me out? Thanks in advance for any help!

ssGSEA2.0.zip

karstenkrug commented 3 years ago

Hi,

Please reach out to the devs of the GSEA gene pattern module: https://github.com/GSEA-MSigDB/ssGSEA-gpmodule

Thanks, K