Hi -
Sorry for the late response. The p-values from LEfSe do require some kind of multiple comparison control, if you’re not using any other biological substructure. But if you do include any of the multiple-class-consistency or directionality tests (i.e. subclass), those can often be more strict than standard MHT correction just by themselves.
darmecian, you correctly pointed out that p-value correction is needed when only KW was performed. LEfSe by default only output significant p-values, whereas multiple comparison correction procedures often require the full list of p-values. To obtain this, you can set the alpha level in LEfSe to a high value (for example, 1), which will make LEfSe output all p-values. This can be performed by setting flag -a 1 in run_lefse.py.
Hope this helps!
Siyuan
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