# Re: [AMBER] How is correlation computed in cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 1 Dec 2021 11:24:44 -0500

Hi,

Could you give the exact cpptraj input you are using, and maybe
describe the data sets you are using. Also, you could send me the data
sets in question off-list and I can try to reproduce the behavior.

-Dan

On Mon, Oct 25, 2021 at 11:07 AM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> I figured out part of my question, so I wanted to update my original post.
>
> The part I now understand: CPPTRAJ does indeed compute the Pearson correlation coefficient, which differs from what Excel reports (via the LINEST function) as R^2, because Excel computes instead the coefficient of determination, which is the square of the Pearson correlation coefficient if there is a single predictor variable (https://www.britannica.com/science/coefficient-of-determination <https://www.britannica.com/science/coefficient-of-determination>).
>
> The part I still donâ€™t understand: What is the meaning of the per-frame output from corr, and how can a given frame have a value > 1.0?
>
> Best,
> Matthew
>
> > On Oct 25, 2021, at 4:45 AM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
> >
> > Dear Amber Community,
> >
> > I am using the corr command in cpptraj to compute the correlation between two data sets, but I am confused over how the correlation at a given frame in the output could be > 1.0. How is the measure of correlation at a given frame being calculated?
> >
> > Also, when I compare the correlation coefficient to what I obtain in, for example Excel with the LINEST function, I get a very different value. How is the correlation coefficient being calculated?
> >
> > Best,
> > Matthew
> >
>
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Received on Wed Dec 01 2021 - 08:30:04 PST
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