Question: [Fwd: Re: automating makeContrasts call in limm]
0
gravatar for Francois Pepin
13.3 years ago by
Francois Pepin1.3k
Francois Pepin1.3k 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 >
go • 606 views
ADD COMMENTlink written 13.3 years ago by Francois Pepin1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 307 users visited in the last hour