How to specify which one is Covariates (control for)?

I am new to MaAslin2, and wish to learn more.
I have microbiome data that I which to find specific taxa that are significantly related to the factor A, B and C (Location is categorical; Factor A, B and C is continuous variable). However, because the microbiome is also environmentally driven, I would like to remove the environmental effect. So I have data similar to the attached table below. My question is: do I need to specifically remove the environmental effect (Location), if yes, how should I do this? I am using the code below (as I want to look at significant microbiome related to all the factor A, B and C):
fit_data= Maaslin2(
input_data = df_input_data,
input_metadata = df_input_metadata,
output = “result”)

Thank you.


Hi @APeh ,

First of all thanks for taking interest in our tool. I would suggest checking out the tutorial found here: MaAsLin2 · biobakery/biobakery Wiki · GitHub and the user manual found here: GitHub - biobakery/Maaslin2: MaAsLin2: Microbiome Multivariate Association with Linear Models.

To answer your question I would suggest implementing a model with fixed effects for all three factors and your location.

Fixed effects can be specified using the fixed_effects

Jacob Nearing