Hello, I found this post from a previous conversation in the previous google groups forum that essentially gets exactly at what I want to know and was never answered, so I am hoping to re-open the query here with credit to the original poser of the question Juan Escobar:
I’m a LEfSe user since long time. My colleagues and I recently submitted a paper with some LEfSe results. One of the reviewers asks us to correct such results for multiple comparisons. I can calculate q-values with R but my question is more fundamental. Do you think it’s necessary to correct for FDR the output of LEfSe? I mean, the algorithm is super strict in choosing biomarkers: first Kruskal-Wallis test to choose features differentially distributed among classes, next pairwise Wilcoxon test applied to the retained features and finally LDA bootstrapping support. FDR control should be performed on each step then. I’m aware of a paper you recently published (Rooks et al. 2014, The ISME Journal) in which you performed Benjamini & Hochberg FDR correction on LEfSe p-values. However, I’m wondering if such correction is necessary altogether.
Your thoughts on this topic are welcomed since as far as I have followed publication of LEfSe results, no one applies FDR.