Results change based on reference?

Downstream analysis and statistics MaAsLin
1

I am trying to detect differentially abundant species based on body location (for ex: face vs arm vs neck).

Just a simplied example of what I am encountering:
If I choose face as the reference, let’s say I see 2 species different between face and arm and 4 between face and neck. Next, I switch to neck as the reference, for some reason, I may get 2 different between neck and face. This is confusing to me because when I chose face as the reference, I saw 4 different species. Why is this number changing? Is it something to do with the reference chosen? What is the “true” value?

Thank you!

2

Hello,

Apologize for the late response but changing the reference will change the question that you are trying to model. As such coefficients can change and more importantly the p-value distribution can change between your multiple tests which will impact the q-values during FDR correction. I would double check to see if the coefficients are similar (but in opposite directions).

Thanks,
Jacob Nearing