[R] Help in using multcomp.

[Chuck Cleland]

A Ezhil wrote:
> Hi All,
> 
> I am trying use 'multcomp' for multiple comparisons
> after my ANOVA analysis. I have used the following
> code to do ANOVA:
> 
> dat <- matrix(rnorm(45), nrow=5, ncol=9)
> f <- gl(3,3,9, label=c("C", "Tl", "T2"))
> 
> aof <- function(x) {
>         m <- data.frame(f, x);
>         aov(x ~ f, m)
> }
> amod <- apply(dat,1,aof)
> 
> Now, how can I use 'glht' for the above amod. I know
> that I cannot use simply 
> 
> glht(amod, linfct = mcp(f = "Dunnett")). 

  Since amod is a list of models rather than one model, do you want
something like this?

lapply(amod, function(x){summary(glht(x, linfct = mcp(f = "Dunnett")))})

> Also, if I want to use Dunnett for comparing C vs (T1
> and T2), how can I specify this in the glht function.

  How about doing it with user-defined contrasts?

contr <- rbind("C - T1   " = c(-1, 1, 0),
               "C - T2   " = c(-1, 0, 1),
               "C - All T" = c(-1,.5,.5))

lapply(amod, function(x){summary(glht(x, linfct = mcp(f = contr)))})

> Thanks in advance. 
> Regards,
> Ezhil
> 
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-- 
Chuck Cleland, Ph.D.
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