The bioBakery help forum

How are the p-values caculated in Maaslin2 analysis? What statistics is used by this pipeline?

Hello i am curious to learn what statistics is used by this pipeline ? Could you please let me know.

Regards
Santosh

Maaslin2 doesn’t calculate the p-values from scratch, it simply calls the appropriate summary function for the model fitting method being used. Usually something to the effect of coef(summary(fit)) under the hood. You can ctrl+f summary_function in the relevant source file to see exactly which. The FDR values are computed with stats::p.adjust.