Expression Dataset

[sudheshna bodapati]

Hi Anthony,

How are you? I have a question in regards to the gsea analysis for running standard GSEA can I use the TPM matrix  as input I created, it is a normalized expression data or gene_counts from DESEQ analysis but those are not integers, can I manually round these to integers. 

ddsTxi <- DESeqDataSetFromTximport(txi,

                                       colData = colData,

                                       design = ~ Condition)

    print ("Generating TPM matrix ...")

    write.table(exprsn,paste(opt$outpath,opt$condition,'_',opt$treatment,'_vs_',opt$control,'_TPMs.txt',sep = ""),quote = FALSE,sep = "\t")

  }

[Anthony Castanza]

Hello,

TPM is suitable for the "single-sample" methods of GSEA which compute over-representation of sets within a sample's individual expression list, but it is not really normalized correctly for between-sample comparisons. For standard GSEA, we would recommend the standard normalized counts matrix. GSEA does not require the values to be integers though, and they should be used as-is from the DESeq2 internal normalization step (usually something like count(dds, normalized=T)

Let me know if you have any additional questions

-Anthony

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

[sudheshna bodapati]

Thank you so much for your response! This helps a lot.

Best

Sudheshna

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