R help - Mar 2013 - Mantel test for comparing two matrices

Hi everyone,
I have two matrices of 2000x2000 size. They consist of a measurement of
RMSD deviations of a protein structure. The basic question i want
to answer is the following: are there a significant  differences between
the two matrices?
I aim to use the Mantel test. I don't really know if this is a good idea or
if there are better solutions for these mega matrices.

Thanks

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Hi,

A Mantel test doesn't test significant differences between matrices.
It tests for significant correlations between dissimilarities. If your
hypothesis is best expressed in terms of distances, then using the
Mantel test is appropriate.

As for size, 2000 by 2000 is not unmanageable, even if those are raw
data rather than distances already.

Sarah

On Mon, Mar 18, 2013 at 6:23 PM, Houcemeddine Othman <houcemoo at
gmail.com> wrote:
> Hi everyone,
> I have two matrices of 2000x2000 size. They consist of a measurement of
> RMSD deviations of a protein structure. The basic question i want
> to answer is the following: are there a significant  differences between
> the two matrices?
> I aim to use the Mantel test. I don't really know if this is a good
idea or
> if there are better solutions for these mega matrices.
>
> Thanks
>
--
Sarah Goslee
http://www.functionaldiversity.org