I have obtained the results from the sample classifier plug-in. However, I got three questions:
(1) Why do I find more features associated with one microbiome than with the other (i.e. Infested vs Healthy)? I am asking this because I am also interested in finding ASVs associated with the Healthy microbiome.
(2) Why is there no cladogram on top of the heatmap (as with the results from the Parkinson mouse tutorial)?
(3) Since I used a collapsed table, are the results somehow biased? I would not think so since the collapsing is at level 7 (species).
Thanks in advance for your support!!! I highly appreciate it.