Most efficient way to look at taxanomic differences between very heterogenous groups?

Hi all,

Me again -

I am attempting to compare taxonomic differences between 3 groups as a result of a given treatment. When I look at my initial data - their microbiomes are very heterogenous - therefore, I’m trying to do pairwise comparisons. I’ve followed the q2 tutorial and I’ve been able to successfully look at alpha and beta diversity, however, I am having a hard time coming up with a suitable method for looking at taxonomic differences between groups as a result of treatment as their starting microbiomes were all so different. Any advice?

Hi @turtleonaleash,
Your best best is to use ANCOM or DESeq2 in R, where either can be used for testing differential abundance from paired samples. QIIME 2 does not currently supported paired-sample differential abundances tests, though we hope to implement those soon.

1 Like

Thanks so much for the help. I will go see if I can figure out this ANCOM stuff!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.