2 way permanova


I have 16S data from bacterial communities from 3 different oceans and within each ocean, they are separated by the morphology of the host they inhabit. So basically I want to test whether my communities are significantly different based on the two categorical variables (ocean and morphology). I see that I can use one way non parametric test with mothur (e.g. amova), but I wonder if there is any way of running a two way PERMANOVA.


You would need to use the adonis command in R to do a 2-way PERMANOVA.


Thanks for your quick answer Pat,

I assume that I need to input a normalized OTU table (obtained with the sub.sample command) into the adonis function) for the adonis command. And also for any other function in the vegan package (such as metaMDS)?


You should run dist.shared with subsample=XXXX and use the ave.dist file.