Hello, I have some RNA-seq data and I would like to explore genes and their functions (specific module enrichment), potentially linked with another biological parameter. I saw different methods (please see below): could you explain me which one could be the best? And mainly why?
1- GSEA pre-ranked with all DESeq2 log2FC values (Time1 vs Time0) & pearson correlation analysis with significant NES values
2- ssGSEA with all DESeq2 Transcripts per Million (TPM) & ratio Time1 vs Time0 with significant NES values & pearson correlation analysis with the above ratios
3- pearson correlation analysis with significant DESeq2 log2FC values(Time1 vs Time0) & GSEA pre-ranked with correlation results (r values with p<0.05)
Any suggestions/corrections are appreciated! Thanks!