Hello community, this is my first question regarding LEfSe.
I am currently analyzing amplicon sequencing data using LEfSe, and I want to compare relative abundances of taxa between disease state and non-disease state, which I defined as class (in this thread I call it disease1 and non-disease1). Under each class there are subdivisions of classes, which we called disease2 (and non-disease2).
So the input data looks like:
Class: disease1 disease1 disease1 non-disease1 non-disease1 non-disease1
Subclass: disease2 disease2 non-disease2 disease2 disease2 non-disease2
I read the thread below, and found that in such a case we should not use disease2 as subclass, as it is not subdivision of single class (disease2 category span both disease1 and non-disease1).
My question is that when “disease2 under disease1” is thought to be different condition from “disease2 under non-disease1”, is this still recommended not to use disease2 as subclass?
I am a bit confused about this particular circumstance, and any help would be appreciated like paper that using subclasses which is not a subdivision of single class. Thanks in advance.