Ranking the GSEA Results
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?
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Personally, I've never understood ranking by p-values. Once you reach the arbitrary 0.05 threshold, the results is not more significant with a smaller p-value. It's just more unlikely the result is caused by random chance, but this doesn't really mean much. Whereas something like fold change is a measure of effect size. If there isn't a convention for ranking you see in literature in your field, I would suggest ranking any significant result by FC.