I came across multiple posts regarding the pre-ranking metric for GSEA when using RNA seq data. However, there doesn't seem to be a consensus.
Some of the metrics I came across are:-
- sign of log fold change * -log10(p-value[not adjusted p-val])
- logfc shrink values from DESeq2
- Inbuilt signal2noise from GSEA. However, this cannot be used in case of <3 replicates.
What metric do you use for ranking the genes or you know is widely used?