I compare two large data sets (13 observations of 300 and 4000 variables respectively) using Procrustes rotations and Coinertia analyses in R. I am able to generate the plots but struggle with the interpretation of them.

–Where can I find concrete information on how to interpret the plots these methods produce?

–Besides the visual ordinations/plots, for Procrustes there is the protest function yielding a numerical output, and for Coinertia, there’s the Monte Carlo test. How come comparing the same data sets yields a highly significant result in one case and a non-significant result in the other case?

– Are these the right methods given my large data sets?