I have a rather basic question that I’d like to check my understanding on. For comparing conditions, I have a single fixed effect with levels A, B, and C. I can run MaAsLin2 with level A as the reference and see what taxa in B and C are different from A. If I want to essentially do pairwise comparisons and also learn what taxa in B and C are different from each other, as I understand it, I would re-run the analysis with level B (or C) as the reference. Is this correct?
To correct these p-values, I would just combine these results and do the BH correction on the original p-values, yes?
Is there anything wrong with this approach? Is there a better way to go about it?
Thanks for a great tool.