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:[EMAIL PROTECTED] Sent: Sun 3/18/2007 11:07 PM To: Nair, Murlidharan T Cc: r-help@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 <[EMAIL PROTECTED]> 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 > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.