Dear all, I hope everyone is staying healthy.
I have a question regarding beta_group_significance with PERMANOVA followed by pairwise comparisons. Which method does Qiime2 use to correct the p-value (which becomes a q value) for multiple comparisons? I can’t find that in the documentation of beta_group_significance or in the original paper (Anderson MJ, 2001). Does anybody know if this is an FDR correction using Bonferroni, Benjamini & Hochberg or other?
Additionally, in order to obtain R-squared values for each test I perform, do I need to run adonis? How is that different from just running beta_group_significance using PERMANOVA?
Any help is very much appreciated. Stay safe