I use the
DEP package for label-free proteomics analysis. Differential expression (
test_diff) results provide p-values (
p.val) and FDR values (
p.adj), the latter are calculated by
fdrtool using moderated t-statistics of empirical Bayes (
eBayes function in
limma) as input. What is a reason to use the moderated t-statistic, not p-value, to compute FDRs?
The relations between the t-statistic-derived FDRs and the FDRs calculated by adjusting the p-values using the BH method (with
p.adjust(method = "BH") or with
fdrtool::fdrtool(statistic = "pvalue")) seem to depend on a contrast of interest, for some comparisons the t-statistic FDR delivers more differentially expressed proteins, whereas for others the p-value-based FDR provides a lower cut-off (see the figure for 4 different contrasts). I would highly appreciate some feedback regarding those differences. Are both procedures correct to apply for FDR calculations?