Hello!
I have samples that are naturally dominated by a single microbial species, and what we are looking at is the bacterial community surrounding this dominating species. Is it possible to remove the dominant species from the data set somehow so that the stats can be done solely on the accessory community?
Thanks!!
That shouldn't matter if you are using compositional methods (i.e. ANCOM, Gneiss or the new Aitchison distance in q2-diversity)
This is because you have some guarantees of independence between features if you look at log ratios. See Figure 1 in this paper
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