So I ran
core-metrics command in my dataset to get measures of beta and alpha-diversity. Then, I went to significance test for beta-diversity using PERMANOVA.
I was surprised that a plot for Weighted Unifrac such as this:
can produce a significant result for the differences (in fact, p-value is quite low - 0.001). Is there any explanation for it?
From what I am understand, you are confused as to why you have significant differences between your groups but no distinct clustering.
Bod explains this really well here: Help in the interpretation of results of beta diversity
Hope that helps!
Thanks, that indeed is very helpful!!
i can see that blue group is linearly different in PC.