Hi there,
I’d agree with darmecian here. For 1, LEfSe will still perform Wilcoxon unless otherwise specified. For 2, I’d say so. Even in the absence of subclass tests LEfSe still filters for features that a) pass the KW test and b) has strong LDA score support. The two together should provide enough evidence for biomarkers.
Thanks,
Siyuan
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