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.