Lefse without any subclass- still valid?

Downstream analysis and statistics LEfSe
4

Sorry for my late reply. I understand what you mean, and I could not find answer in the thread I specified, as you stated. From my current understanding,

  1. Absence of subclass, LEfSe will perform per-feature KW, and NOT skip wilcoxon unless you specified --wilc option to 0. Instead, LEfSe seem to perform both KW and Wilcoxon between class. I was examining format_input.py and noticed this. I made another thread regarding this (if it is valid for lefse to perform KW and Wilcoxon both between class).
    Question about LEfSe input_format.py when specifing no subclass

  2. I think yes, considered they went through KW and LDA, however, in this case (–wilc 0), the p-value from KW, which is considered to be reported whether wilcoxon is performed or not, is not reported. I additionally asked this problem in the thread above.

Sincerely,