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I have a query regarding the analysis of GSEA Results. I have used GSEA to obtain the dysregulated KEGG pathways. Now, I want to rank the dysregulated KEGG pathways.
I have seen people ranking the dysregulated genes on the basis of log2Fold Change and p-value obtained from DESeq2. For genes, they use the decreasing order of log2FC * (-log10 p-value) to rank the genes.
So, is it logical to use NES * (- log10 Nominal p-value) for ranking the KEGG pathways?