Input files and error

[Parwez Ahmad]

Hi,

I am using RunGSEAPreranked and getting some errors called successful with some errors. I am using list of preranked genes with fold change. I am not getting list of pathways with enrichment score and p values. 

Second question, how to determine which gene set and chip platform to use for our research questions where we wanted to discover the list of genes and pathways associated with chemical exposure in cord blood RSeq data. 

Thank you and looking forward to your valuable suggestions.

Best regards,

Parwez

[Anthony Castanza]

Hi Parwez,

Unfortunately without more information the amount of help I can provide is limited.

Please send the full text of any error messages you received (you might need to expand the dialogue details). This will help us identify the issue you're having.

A screenshot of your Run GSEA Preranked window would also help us by allowing us to see any parameter options you've configured.

Additionally, in order to recommend a chip file, I'd need to see a sampling of the IDs from your input file.

For picking the gene sets, that is something you'd need to determine yourself based on the specifics of your research questions, you can explore our full offerings with additional details on the MSigDB website: https://msigdb.org.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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