I am a little bit confused about how AMOVA and HOMOVA differ. I understand that AMOVA tells you whether there is a significant difference between the centroids of groups but I’m struggling to understand what HOMOVA tells you.
When would you choose to use one test over the other?
My analogy is that if you wanted to know whether men and women had different heights, you’d want to know whether the mean height of men is different than the mean heigh of women given the variation in their heights. You’d probably use a T-test or by analogy, AMOVA. Say you didn’t care about their mean heights, but were rather interested in whether there was a significant amount of variation in their heights. Does the standard deviation of men’s heights differ from the SD of women’s heights? Here you’d probably use Bartlett’s test for homogeneity of variance. For microbiome data we use HOMOVA to see whether the spread in the data is different between groups. We’ve used this type of test to look at differences in stability.
Hope this helps…