Late, I know, but if method comparison id the interest, the methcomp package on 
CRAN does Bland-Altman plots and passing-Bablock regression, both clinical 
chemistry staples for method comparison.

S Ellison

> -----Original Message-----
> From: r-help-boun...@r-project.org 
> [mailto:r-help-boun...@r-project.org] On Behalf Of Pedro Mardones
> Sent: 21 September 2011 19:12
> To: Marc Schwartz
> Cc: R-help@r-project.org
> Subject: Re: [R] help in interpreting paired t-test
> 
> Thanks for all the replies and comments. I've followed Marc's 
> suggestion of using the Bland-Altman's approach which I found 
> pretty clarifying for comparing data collected on the same subjects.
> 
> BR,
> PM
> *******************************************************************
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