I have been encountering a puzzling phenomenon when performing PERMANOVA tests with
beta-group-significance in Qiime2 (v2018.2). The p-value for tests performed in Qiime2 are consistently lower than the results from the
adonis function in the R package vegan. This is true for several data sets, but I have documented the analysis for one dataset at: https://github.com/maggimars/MicrobiomeSelection.
For this particular example, the
adonis p-value for between group differences is 0.023, the R-squared is 0.506 and the F.Model is 2.0557. When the same analysis is repeated with Qiime2
beta-group-significance, the p-value is 0.003 and the psuedo-F is 3.0469.
I was under the impression that
adonis and PERMANOVA in Qiime2 should yield the same results. Is there a simple reason why I may be seeing different results with the two methods?