Hi there -
I’m trying to reconcile a few discussions on LEfSe and multiple testing corrections.
Regarding the -s parameter that can be set as discussed above - what type of multiple testing correction is performed when the independent tests (-s 1) option is selected?
Elsewhere in the support forum, it seems that multiple testing corrections was not previously baked into LEfSe (?) and so folks were running the run_lefse.py with the alpha set high (ie -a 1) to then take the output to do multiple testing correction with a different tool (ie p.adjust in R).
So as of now (2022), can we reasonably report multiple testing corrections have been performed if we run with the -s 1 option as above?
I’d also like to open the discussion regarding necessity of multiple testing corrections when we’ve got 3 different phases (Anova for class, KW for subclass, and LDA for effect size)