I have had a look through the forum and these pages but I am still a bit confused so would appreciate some clarification on the PERMANOVA statistics.
I have run the following command: https://docs.qiime2.org/2020.2/plugins/available/diversity/beta-group-significance/
using the pairwise option.
To simplify, I have two groups called A and B:
I want to know what the statistics output means at the bottom of the output page
|Group 1||Group 2||Sample size||Permutations||pseudo-F||p-value||q-value|
The answers previously on the forum say: " The pairwise permanova results at the bottom of the page compares between Group 1 and Group 2, and tests to see if they are statistically significantly different."
From my diagram above I am taking this to mean the statistics are referring to the difference between the within distances observed for A and the within distances observed for B (comparison 1) in the diagram. Is this correct?
If so, is it possible at all to perform PERMANOVA on comparisons 2 and 3 above or should I be using a different test (there was a Monte Carlo permutations 999 option in QIIME 1 previously but what should I be using in QIIME 2?). These values would be more informative to me because in theory the within distance could be very similar but the between distance very different meaning the samples form two distinct clusters but this might not be picked up if only comparison 1 was performed.
I have the plots for comparisons 1, 2 and 3 though.
Any advice or clarification much appreciated.