This is similar to the question posted in this thread, which has been closed·

Q2 PERMANOVA p-vals consistently lower than Vegan Adonis p-vals for the same data set and variable (Q2 PERMANOVA p-vals consistently lower than Vegan Adonis p-vals for the same data set and variable)

Hi!

I am new to qiime2 and microbiome analysis in general. I was interested in my unweighted unifrac result from qiime2 because significance testing with PERMANOVA showed pairwise differences all throughout my 3 groups. So I wanted to reproduce the results in R: I used phyloseq to do a PCoA plot (which was more or less the same as the q2 output, just a little different %ages in axes), but when I performed significance testing with pairwise adonis (as I learned was the equivalent of PERMANOVA in R) on the distance matrix, the p values I got were different such that 1 pairwise comparison was no longer significant.

So I tried running pairwise adonis again in PERMANOVA /but/ using the exported distance matrix from unweighted unifrac (with formatting modifications) result in qiime2, and I got significant results for all 3 pairwise comparisons.

My question is, why is the distance matrix from qiime2 different from that produced in phyloseq in R (phyloseq::distance)?

And,

would it be all right to use the phyloseq output for PCoA (using phyloseq ordinate function on physeq object) together with the adonis pairwise output run on the exported distance matrix of the qiime2 output?

Thank you!