Question about ANCOM BC2

[colinbrislawn (Colin J Brislawn)]

@Themis80

if this was a standard t test, I would have to use a paired t test to compare baseline and follow up.

Here's an example using a diet-swap cohort. This sounds very similar to your project!

https://www.bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html#run-ancom-bc2-on-a-real-longitudinal-dataset

(I've moved this to Other Bioinformatics Tools because there's not a qiime plugin for ANCOM-BC2... yet!)