Hi Gordon, I should mention that the behavior is different with R 2.2, but it still doesn't work. > myContrasts<-c("t1-t2","t1-3","t2-t3") > contrast.matrix<-makeContrasts(myContrasts,levels=design) Error in eval(expr, envir, enclos) : object "myContrasts" not found > traceback() 3: eval(expr, envir, enclos) 2: eval(ej, envir = levelsenv) 1: makeContrasts(myContrasts, levels = design) > sessionInfo() R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: limma "2.3.7" I don't have any machine with R 2.3, but I could install it. Francois On Mon, 2006-03-13 at 11:31 -0500, Francois Pepin wrote: > > > Ideally, I would want to have a way to do: > > > > > > myContrasts<-c("t1-t2","t1-3","t2-t3") > > > contrast.matrix<-makeContrasts(myContrasts,levels=design) > > > > Your question isn't clear, at least not to me. What is wrong with the code you've just given? > > Sorry, I thought this was a well-known "feature" of the makeContrasts > function, so I didn't go into the details. > > So to complete the toy example with 3 treatments and dye swaps of each: > > > design > t1 t2 t3 > [1,] -1 0 0 > [2,] 1 0 0 > [3,] 0 -1 0 > [4,] 0 1 0 > [5,] 0 0 -1 > [6,] 0 0 1 > > > myContrasts > [1] "t1-t2" "t1-3" "t2-t3" > > > contrast.matrix<-makeContrasts(myContrasts,levels=design) > > contrast.matrix > myContrasts > t1 "t1-t2" > t2 "t1-3" > t3 "t2-t3" > > Which doesn't make for a usable design matrix. The expected behavior is: > > > contrast.matrix<-makeContrasts("t1-t2","t1-t3","t2-t3",levels=design) > > contrast.matrix > t1-t2 t1-t3 t2-t3 > t1 1 1 0 > t2 -1 0 1 > t3 0 -1 -1 > > > sessionInfo() > R version 2.1.0, 2005-04-18, x86_64-unknown-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "base" > > other attached packages: > limma > "1.9.6" > > > > > Is your question that you'd like to compute all pairwise comparisons between hundreds of different > > treatments or patients? > > No. I have tumors and normal samples for each patient. One of the things > I'd like to do is tumor vs normal for all each of the patients. Another > would be to automate the comparisons between clinical variables. It's > just cumbersome (and error-prone) to do by hand when there are over 50 > patients. > > Francois > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >