Hi,
I am fairly new using MaAsLin2 and was wondering how comparison between conditions is working. I have three groups (let’s call them A, B and C) in my condition fixed effect, and when I look at the results, they are shown with only two of my groups as value. Does that mean that MaAsLin only compares groups with the reference (A vs B and A vs C) or does it also compares all groups between them (A vs B vs C)?
Thank you,
Mathieu