Problem creating a contrast matrix
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@siarhei-manakou-2255
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@james-w-macdonald-5106
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Hi Sergei, You can't start a variable name with a number in R, so you can either change to something like day.025, or you can construct your contrasts matrix by hand, using something like contrast <- matrix(c(-1,0,0,1,0,0,0,-1,0,0,0,1,0,0,-1,0,0,0,0,1,0,-1,0,0,0,0,0,0,1 ), ncol=4, dimnames=list(colnames(design), paste(colnames(design)[c(4:7)], colnames(design)[1])) I often construct the contrasts matrix by hand as it gives you more control over the dimnames attribute. Best, Jim BTW, you only need to send a question once. Sending it thrice may well result in no response ;-D Siarhei Manakou wrote: > Hello, > > Im a first year PhD student in Sanger institute - just started working with bioconductor and encoutered problem while building a contrast matrix. I first made the desing matrix: > > >> design<-model.matrix(~-1 + pData(eset)$days) >> colnames(design)<-levels(pData(eset)$days) >> colnames(design) >> > [1] "025days" "12days" "16days" "1days" "2days" "4days" "8days" > > > Then attempted to make a contrast matrix: > > >> contr_matrix<-makeContrasts(1days-025days, 2days-025days, 4days- 025days, 8days-025days, 12days-025days, 16days-025days, levels=design) >> > > but it produces the following error message: > > Error: syntax error, unexpected SYMBOL, expecting ',' in "contr_matrix<-makeContrasts(1days" > > I would be very grateful if somebody could point out what the problem could be. I am using R-2.5.0 under Linux. > > Thanks a lot! > Sergei > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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