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Jun 18, 2012 at 14:41 comment added Jdub In R there is the function adonis in the package Vegan that performs permutational multivariate ANOVA. This will generate a statistical test to tell you whether method A is different from method B. This package comes out of plant ecology where you count multiple species (the variables) in different small plots. Related to this is AMOVA, analysis of molecular variance, where the variables are molecular data. For this you can use the R package ade4, but there is other free and online software you can find at the link.
Jun 16, 2012 at 14:33 history answered AnastD CC BY-SA 3.0