Hello, I google a lot but still confusing. First what's the major difference we get difference expression matrix(
limma::lmFit) before gene name annotation, not annotate gene name to expression matrix then call diff-expr.
Second, how to choose strategy to handle multiple probes mapped to same gene? Some use average value, some use mean and some may use largest value. If I care whole gene, maybe average and mean value is better. But if I call diff-expr matirx on probe level, then I merge(combind) multiple probes data to one gene, I don't thinks is appropriate to average
P.val . Can you share your experience here? Thanks.