[R] multcomp

[Nair, Murlidharan T]

Thanks for the hint. 
Here is what I had done earlier according to the old package
 
 mult.comp<-simint(a~b, data=z, conf.level=0.99, type=c("Tukey") )
 isoforms<-as.vector(rownames(mult.comp$estimate))
 estimate<-as.vector(mult.comp$estimate)
 lower<-as.vector(mult.comp$conf.int[,1])
 upper<-as.vector(mult.comp$conf.int[,2])
 p.val.raw<-as.vector(mult.comp$p.value.raw)
 
Here is how I modified the above so that I can use the new package. Can someone comment if what I have done is correct or not?
amod<-aov(a~b, data=z)
mult.comp<-glht(amod, linfct=mcp(b="Tukey"))
estimate<-confint(mult.comp)[1,1]
lower<-confint(mult.comp)[1,2]
upper<-confint(mult.comp)[1,3]
summary(mult.comp) does give the adjusted pvalues.  I tried all the subscripts to extract it to store in a variable but could not, can any one help me here. Also,  how do I specify the conf.level to be equal to 0.99. The default is 0.95
 
Thanks for your help,
Cheers../Murli

 
________________________________

From: talepanda [mailto:talepanda at gmail.com]
Sent: Sun 3/18/2007 11:07 PM
To: Nair, Murlidharan T
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] multcomp



?glht says
>with 'print', 'summary',  'confint', 'coef' and 'vcov'  methods
>being available.

try:

example(glht)
summary(glht(amod, linfct = mcp(tension = "Tukey")))
confint(glht(amod, linfct = mcp(tension = "Tukey")))

On 3/19/07, Nair, Murlidharan T <mnair at iusb.edu> wrote:
> I used the multcomp package sometime back for doing multiple
> comparisons. I see that it has been updated and the methods like simint
> are no longer supported. When I run the program it prompts to me to use
> glht. How do I get the lower and upper conf int and the pValues using
> glht? Does anyone have an example?
>
> Thanks ../Murli
>
>
>
>
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