In one of the datasets, I have 3 different treatments (Trt1, Trt2, Trt3), with significant differences in beta diversity metrics (PERMANOVA). Now I would like to find out which genera or ASVs are contributing to those differences. My plan is to use Aldex2 to find differentials between Trt1 and Trt2, Trt1 and Trt3, Trt2 and Trt3, and plot differentials in 1 figure.
I know that Aldex2 can perform adjustment of p-values for multiple comparisons under the hood. But since I would like to pool differentials from 3 independent Aldex2 runs, should I extract all p-values of all features before the adjustment (not only significant), pool them in one table and then perform correction to find differentials, or I can just use already corrected p-values and differentials from each Aldex2 run?
I really hope that I explained my question well