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!