A similar but not identical query already exists in the forum however it wasnt explained in detail so I am posting my query here.
I am trying to use the lefse for finding group of taxa which can successfully classify two disease groups from each other. As far as I understand, Lefse uses factorial KW rank sum test to select features that are differentially abundant between the two classes (say disease 1 and disease 2) and it used Wilcoxon test to further screen features which are consistently differentially abundant between the subclasses.
However in my dataset, there are no subclasses. In that case does Lefse skips Wilcoxon test ? And if it does, then are the selected biomarkers at the end of Lefse considered successful biomarkers or not?
Thank you for the help.