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@user-24811
Last seen 3.7 years ago
I am trying to do differential abundance in DESeq2 on my 16s rRNA amplicons. The design of my experiment is Y ~ treatment (as fixed effect factor) + body_site (as fixed effect factor) + treatment*body_site + block (random effect factor). I can't see any argument on the vintage for assigning a random effect factor in my model.
Is it even possible to do linear mixed effect model in DESeq2?
Moreover, I am also interested in seeing the differences in different taxa levels. But, by default the results gives me all the 7 taxa levels. How can I revoke the results of only for phylum or family taxa? Not for their sub-taxa (e.g. down to species).
Much appreciated in advanced.
Thanks Michael Love
I would be appreciated if you could give me a hint on how to use deseq2 for different taxa levels. By default, it gives the results of all taxa at once. While I am interested in knowing the changes at e.g. Order or Family.
Kinds, Farhad
I don't actually think DESeq2 is a good fit for microbiome data, and don't have any particular recommendations for using it in this context.