When using LEfSe without subclasses

Dear all.

Hi. I’m working on a dataset including microbiome data and clinical data.
I want to analysis difference of abundance across clinical parameters,(disease, sex, age…)

As far as i know, LEfSe does 2 statistical test, of which one uses class and the other use subclass.
My question is… when a dataset have no subclasses to compare, could i use LEfSe algorithm?

My colleague showed a ancom analysis result on the same dataset and i found the lefse result show me much more otus than the ancom analysis…


Hi @Crispy13,

I’ve moved this to “other tools”, since LEfSe isn’t in QIIME, or part of a QIIME plugin AFAIK.


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Hi @Crispy13,

My understanding is that defining a “subclass” is optional. That is when you can subdivide your data in such a way that your…

subclasses should be subsidiaries or subdivisions of a single Class

Check out the phrasing of these posts form the LEfSe-users group and QIIME 2 forum:

-Best wishes!


Thank you for reply!
So, not using subclasses is not a problem…

If a class is bahaviors(or symptoms) of disease, is it make sense to designate prognosis as a subclass?