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

(Jacqueline B) #1

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?

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(Nicholas Bokulich) #2

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.

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(Jacqueline B) #3

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

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(system) closed #4

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