Interaction term for 3 groups and q value

Hi, I plan to run Maaslin2 with linear mixed model to investigate the study the effects of different diets on microbiome features across 2 timepoints. May I know if I would like to include group, timepoint and their interaction term, how can I construct the interaction term?

3 Groups (diet) = Group A (reference), Group B and Group C
2 Timepoints = Baseline (reference) and Endpoint

Also, do I need to filter out the interaction term to recalculate the q values before selecting the features with significant interaction term (q value < 0.25)?

Thank you!


You check out this link here: MaAsLin2 · biobakery/biobakery Wiki · GitHub.

It shows how to construct interaction terms that can be then passed into Maaslin2 as fixed effects. I am not sure what you mean by filtering out the q values before selecting features. If you are running that many tests and planning to look across all the variables tested then no filtering should be needed.

Jacob Nearing