The bioBakery help forum

If I set the LDA score below the default value of 2.0, is it still statistically reliable?

I understood about LEfSe analysis(KW, Wilcoxon), but still not sure that can I adjust the default score.

Our data shows very few different species in score>2.0 . (Independent variable is two, before and after.)
So I want to adjust the default score. There are no problem?

please help me.

It is fine to change the default value for the LDA score; it is a measure of effect size, not statistical significance. Any features plotted will be statistically different.