Paired analysis of differential relative abundance

Hi, how can I do a paired analysis between samples of differential relative abundance of OTUs in the MDP module (MicrobiomeAnalyst)? I want to compare the relative abundance before and after treatment, so need to pair samples - I can’t find any option for this under “single factor comparison”, only unpaired options . Would appreciate any advise. thanks.

You need to use the multi-factor analysis for this (you have two variables/factors: treatment and subject). To model your Sample ID as a random effect, specify it under ‘Blocking Factor’ and to model as fixed effect specify it under ‘Covariates (control for)’, and put your Treatment variable as ‘Primary Metadata’. Here is shown for modeling ‘Subject’ as a random effect for the example dataset #1:

Specifying as a ‘Blocking Factor’ is more typical for paired analysis, however the R package we use has some more strict sample size/balanced dataset requirements for random effects modeling. If it’s not compatible with your dataset (you’ll get a message), try specifying as a ‘Covariate’ as this will also account for paired relationships.