I am a bit confused with GSEA and I was hoping that you could help me. I've got RNA-Seq data (two conditions with 5 replicates each). The GSEA website says that the suggested method is the standard one vs the pre-ranked so I decided to give it a try. I have read the following on this paper: "Gene set permutation is recommended for studies with limited variability and biological replicates (i.e., two to five per condition). In this case, differential gene expression values should be computed outside of GSEA, using methods that include variance stabilization (such as edgeR29, DESeq30 and limma/voom31,32) and imported into the GSEA software before pathway analysis."
I'm not sure, should I do a standard GSEA with phenotype or a gene set permutation?