Hi all, especially @mortonjt ,
I’m trying to figure out Songbird on paired samples. Ive been through the tutorial and looked at the differential code from the original paper. Im slightly confused how to use this for paired samples, since as far as I can tell by the formula, the code is looking at a bulk comparison between before and after tooth brushing without conditioning on the individual. (The code is
C(brushing_event) and I might have expected something closer to the
(C(brushing_event) | host_subject_id) in an LME… except that I m not totally sure that works in this model.) I might also be missing something with pre-processing where the pairwise comparison is already set up.
Alternatively, if there is another kosher way to do paired sample tests for relative abundance deltas, that would be super useful. I found one paper, but it was a UniFrac-like approach and I’d like differential abundance for individual features or clades.