Multiple group comparisons within one sole mmvec analysis

[natalie-melendez]

Hi,

Currently, I want to compare microbial/metabolome integration from several groups in one sole analysis (one biom that contains all the samples from the different groups). Is this possible? Or must I perform each group analysis individually?

[mortonjt]

I'm having trouble understanding this question, can you clarify?
It is not uncommon to split up biom tables into multiple smaller files to run MMvec on individually

[natalie-melendez]

Hi @mortonjt! Sure, I will clarify. Currently I want to analyze in one sole analysis the samples from 4 different mice groups: healthy (n=10), tumor-implanted (n=10), short term treated (n=4) and long-term treated (n=6). From what I saw in other forums, it would be impossible to run these groups individually as they are small. Therefore, I wanted to do it in 1 biom that contained all the samples. However, is there a way to include a metadata column in order to add the category of the treatment? For example, that I may be able to visualize my emperor plot but adding the category as a shape to be able to distinguish the metabolites according to this treatment variable?

[mortonjt]

Got it. Yes normally I run MMvec on all of the samples, and run differential abundance analysis to color the coordinates in Emperor.

I had a tutorial here on how to do this with Songbird differential abundance analysis : https://github.com/mortonjt/q2stats-workshops/blob/master/lessons/multiomics.md

It can probably be done with other tools like aldex2, ancombc, but I'm not sure about their output formats.