Hi, I have a question about the MSEA QEA analysis. Does the enrichment analysis use normalized data or original data when calculating enrichment scores and p values? In addition, how do you know which group is compared to the other (ex: A compared to B vs B compared to A) when looking at the Top 25 enriched metabolite sets?
For Q1: this depends on your choice when you perform data normalization;
For Q2: please read this post