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).
A general note - please post one question per topic - combing multiple questions like this becomes problematic for support (each question might need a separate response), and also is very difficult for others to search for.
Wow, that is a huge question, and probably is worthy of a publication on it's own. How about you think of some more specific questions, and we can help you with those. Please post these as new question posts.
You haven't provided us with any information about what you have done - what version of QIIME 2 are you using? What command did you run? Copy and paste, please.
Please ask this in a new question post (and please provide much more information, it isn't clear to me what you're looking for.
