Dear Bioconductor List, I am using limma to fit a linear model with what I believe is called a disconnected design: > data <- ReadAffy() > eset<-rma(data) > design<-model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4))) > colnames(design) <- c("1A_L5V4_No_Pon_A","1C_L5V4_Pon_A_DHT_24hrs","2A_L5S2_No_Pon_A","2C_ L5 S2_Pon_A_DHT_24hrs") > fit<-lmFit(eset,design) > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs -2A_L5S2_No_Pon_A -1C_L5V4_Pon_A_DHT_24hrs +1A_L5V4_No_Pon_A,levels=design) I get the error message: Error: syntax error in " contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs" I would greatly appreciate any suggestions. Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In memoriam, John Stewart Williamson

Richard Friedman <friedman at="" cancercenter.columbia.edu=""> writes: > Dear Bioconductor List, > > I am using limma to fit a linear model with what > I believe is called a disconnected design: > > > > data <- ReadAffy() > > eset<-rma(data) > > design<-model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4))) > > colnames(design) > <- > c("1A_L5V4_No_Pon_A","1C_L5V4_Pon_A_DHT_24hrs","2A_L5S2_No_Pon_A","2 C_L5 > S2_Pon_A_DHT_24hrs") > > fit<-lmFit(eset,design) > > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs > -2A_L5S2_No_Pon_A -1C_L5V4_Pon_A_DHT_24hrs > +1A_L5V4_No_Pon_A,levels=design) > > I get the error message: > > Error: syntax error in " > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs" > > I would greatly appreciate any suggestions. I suspect the issue is that symbols in R (variable names) cannot begin with numbers and so 2C_L5S2_Pon_A_DHT_24hrs is perhaps a bad choice. Does the error go away if you do something like: colnames(design) <- paste("x", colnames(design), sep="") + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Hi Richard, the problem is with the names of your samples. Limma treats the sample names as R variables when it makes the contrast, and R variables cannot start with digits. Just add a letter in front when setting the colnames of the design matrix and when doing the contrast and it should get rid of the error. Francois On Wed, 2007-04-11 at 17:58 -0400, Richard Friedman wrote: > Dear Bioconductor List, > > I am using limma to fit a linear model with what > I believe is called a disconnected design: > > > > data <- ReadAffy() > > eset<-rma(data) > > design<-model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4))) > > colnames(design) > <- > c("1A_L5V4_No_Pon_A","1C_L5V4_Pon_A_DHT_24hrs","2A_L5S2_No_Pon_A","2 C_L5 > S2_Pon_A_DHT_24hrs") > > fit<-lmFit(eset,design) > > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs > -2A_L5S2_No_Pon_A -1C_L5V4_Pon_A_DHT_24hrs > +1A_L5V4_No_Pon_A,levels=design) > > I get the error message: > > Error: syntax error in " > contrast.matrix<-makeContrasts(2C_L5S2_Pon_A_DHT_24hrs" > > I would greatly appreciate any suggestions. > > Thanks and best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In memoriam, John Stewart Williamson > > _______________________________________________ > 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