Hi Jun, >> I have three levels for a factor names "StdLot" and want to make three >> comparisons, 1 vs 2, 1 vs 3 and 2 vs 3.
With only three levels to your factor, the contrast matrix you are specifying is over-parametrized (i.e. over-specified): it has 3 rows and 3 columns. ## Look at the default behaviour contrasts(d3$StdLot) <- NULL contrasts(d3$StdLot) contrasts(d3$StdLot) <- contr.helmert contrasts(d3$StdLot) I think what you really want are linear contrasts, which you will find in package car (?linear.hypothesis), in gmodels (?estimable) [based on Frank Harrell's approach; so look at his package Design], and package multcomp, amongst others. Regards, Mark. Jun Shen-3 wrote: > > Would like to try my luck to see if I can catch your eyes. > > I was trying to do some contrasts within ANOVA. I searched the archive and > found a clue posted by Steffen Katzner > ( http://tolstoy.newcastle.edu.au/R/help/06/01/19385.html) > > I have three levels for a factor names "StdLot" and want to make three > comparisons, 1 vs 2, 1 vs 3 and 2 vs 3. > > First, > contrasts(d3$StdLot,3)<-matrix(c(1,-1, 0,0,1,-1,1,0,-1),3,3) #d3 is the > data set. set up the contrast matrix > > Second, > aov(Bkg~StdLot,na.rm=T,data=d3,contrasts=contrasts(d3$StdLot))->mod.aov > #ANOVA, > > Finally, > summary(mod.aov,split=list(StdLot=list('1 vs 2'=1,'2 vs 3'=2,'1 vs 3'=3))) > #comparison summary > > Here is the final result I got, the third comparison is missing. Does > anyone > have any idea what is wrong here? If I change the order of the comparisons > it's always the third one missing. So I guess it's not due to the data. > Appreciate any comment. > > Df Sum Sq Mean Sq F value Pr(>F) > StdLot 2 1.905 0.953 10.3769 3.710e-05 *** > StdLot: 1 vs 2 1 0.223 0.223 2.4239 0.1200 > StdLot: 2 vs 3 1 1.683 1.683 18.3299 2.162e-05 *** > StdLot: 1 vs 3 1 > Residuals 601 55.173 0.092 > --- > Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > 2 observations deleted due to missingness > > > -- > Jun Shen PhD > PK/PD Scientist > BioPharma Services > Millipore Corporation > 15 Research Park Dr. > St Charles, MO 63304 > Direct: 636-720-1589 > > [[alternative HTML version deleted]] > > > ______________________________________________ > [email protected] 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. > > -- View this message in context: http://www.nabble.com/Contrasts-within-ANOVA-frame-%28Repost%29-tp25052361p25057955.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ [email protected] 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.
