Hello greetings to all, Here, I have the same questions? The excell of my DEG data have different values such as read count, TPM, FPKM, N of individuals samples in a certain group. Thus which values we will use to analyze the GSEA? Thank you,
According to the Broad institute guidelines you should run GSEA using a non-pre-ranked method. For this purpose, if you are analyzing your data with DESeq2 or edgeR packages you must retrieve and use normalized counts using the median of ratios or TMM methods, respectively. Both methods make comparable dataset among samples. Avoid using raw counts, TPM or FPKM because the last normalization methods are not aware of library composition.