Hi eveyrone, Thanks to Carolyn Fitzsimmons for pointing out that there was indeed a bug in that code. The behavior on R 2.2 is indeed the same as with R 2.1. Sorry about that. Francois On Mon, 2006-03-13 at 11:53 -0500, Francois Pepin wrote: > 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 > >

Hi Francois, I think that you are asking for makeContrasts() to accept a character vector of contrasts. At the moment, it expects contrasts to be specified via expressions, character strings or character vectors of length 1. In fact, even the treatment of character vectors of length 1 has been somewhat unstable, partly because of changes to what is permissible for new.env() calls in R 2.3. I will look into making the makeContrasts() more predictable in terms of character variable arguments. Once that is done a solution to your problem should be simple. In the meantime, you might consider using paste() to assemble your makeContrasts() call as a character string, and then evaluate it using eval(). This would allow you to program it (entirely in R) instead of entering it at the interactive prompt. Best Gordon Francois Pepin wrote: >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=desig n) >>>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 >> >>