The bioBakery help forum

Question about group comparison

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.Bellerose you are right - by constructing dummy coding, MaAsLin2 compares the reference category with other categories. As a result, you will always see (K-1) categories in the final table for any categorical variable with K categories (minus the reference category).