Taxonomy difference between 2 time points?

[Nicholas_Bokulich]

Hi @thompsrs,
Welcome to the QIIME 2 forum!

@thompsrs

I’m interested in getting the difference (or changes) in taxonomy between 2 time points and then running ANCOM on those differences.

You have the correct command for looking at paired-sample changes across a time interval, and technically it could be performed on specific features in a feature table... but there are two issues to be aware of:

1. it sounds like you are interested in discovering which of many features change in relative frequency, not testing specific features. This action will only test specific features one at a time...
2. this action does not perform any transformation on the data, so on its own a paired Wilcoxon or t-test is not really an appropriate test for compositional data (e.g., relative frequencies). Technically you could transform the data with an appropriate method and then input those data to this action, but this is not possible in QIIME 2 at the moment on its own.

For paired testing with ANCOM it is easiest to test outside of QIIME 2 at the moment... this is a recent relevant discussion, including a simple way to do this with python/scikit-bio:

Differential abundance analysis (e.g. ANCOM) for paired samples (e.g. normal tissue vs. tumor tissue from cancer patients)

Neat study! Seems plausible Not at the moment Yep! This is a matter of post age... in the first few releases of q2-composition it was technically possible to do a paired test with ANCOM but the test option was removed in later releases. Yes — not in QIIME 2 (as far as I know), but aldex2 would be a good solution in R, as a matter of fact here's the relevant documentation: Perhaps @dgiguer can let us know if a paired test is also possible with q2-aldex2, but I could not find it from a …

Good luck!