Divergences between PERMANOVA results


I’m simultaneously running my 16S dataset in MicrobiomeAnalyst and my script using phyloseq and vegan to compare results. Using my unfiltered, unnormalized data, I had the exact PCOA ordination with Bray-Curtis dissimilarity, but different results for the PERMANOVA p-value: 0.08 from MicrobiomeAnalyst against 0.32 from vegan::adonis2 (formula = bray_bac ~ sample_data(ps_bac)$Treatment, permutations = 999)

What might be causing this difference? For what is worth, I ran an ITS2 dataset and found similar results in both MA and my script.

MicrobiomeAnalyst computes within a comprehensive workflow. It is possible that the previous steps (data filtering, normalization, etc) will change the underlying data. You can refer to the MicrobiomeAnalystR package and R command history generated during your analysis