[R] similar limma's contrasts.fit() for lme (mixed effect model)object

[shirley zhang]

Hi Max,

Thanks for your prompt reply. Actually I have already checked contrast
package, but I still could not figure out how to set the contrast
matrix for a 2x2 factorial design.

I would like to set a contrast exactly similar to the limma's user
guide, 8.7 Factorial Designs (page 45). For example, after a mixed
linear model fit with the default contr.treatment, I want to compute
an estimated coefficient as the sum of the third and fourth
coefficients of the original lme model (2x2 factorial design).

Could you give me an example how to implement this using  the contrast package?

Thanks,
Shirley

On 7/9/07, Kuhn, Max <Max.Kuhn at pfizer.com> wrote:
> Shirley,
>
> The contrast package can do this. The method of specifying the contrast
> conditions/coefficients is different (and I think easier).
>
> Max
>
>
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of shirley zhang
> Sent: Monday, July 09, 2007 11:16 AM
> To: R-help at stat.math.ethz.ch
> Subject: [R] similar limma's contrasts.fit() for lme (mixed effect
> model)object
>
> Dear R help,
>
> In limma package, contrasts.fit() function is very useful. I am
> wondering whether there is a similar function for lme object, which
> means given a mixed linear model fit, compute estimated coefficients
> and standard errors for a given set of contrasts.
>
> Thanks,
> Shirley
>
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