Time + treatement effects

[Nicheca]

@Nicholas_Bokulich

I would discourage that approach. If you are trying to determine what differs by treatment, then this comparison of what changed over time and essentially making a venn diagram of those changes would not be a rigorous enough approach. If anything, I’d recommend running ANCOM to compare treatments at your two individual time points.

If you really want to assess the interaction between time and treatment, then you could try out q2-gneiss. But I assume treatment effects are probably the main concern here, in which case splitting up your data by time would be an easy to run and interpret approach.

Thank you so much @Nicholas_Bokulich! My last idea was to use the log2FC (between my 2 time points) and look at the treatment effect with ANCOM. Not appropriate neither?
I am working on the q2-gneiss and will give a try as rhapsody!

It is difficult to find the best way to analyze these data because actually I am equally interested by the time AND the treatment effect! 2 different questions but I would love to address both!