Hello Biostars, Can anyone tell me how to prepare input data set for GSEA after Differential Gene Expression Analysis by DESeq2? How will I rank the genes? Should I rank based on log2FC or Adjusted P value? Is there any way to generate a GSEA ready data directly from DESeq2?. I was using topGo for gene ontology enrichment analysis before and recently came across GSEA. Which one is better GO enrichment analysis or GSEA? Even after going through the papers I couldn't find a significant difference between above two.
Thank you
I like DESeq2. It would be great to have in the future something like ROAST/CAMERA/GSEA in DESeq2 too!