Hi group, I have a patient dataset of 6 control and 11 disease. so the code that I have written is: >library(affy) >library(limma) >eset<-as.matrix(read.table("GSEXXXX_series_matrix.txt",header = TRUE,sep = "\t", row.names = 1, as.is = TRUE) > design <- model.matrix(~-1 + factor(c(1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2))) > fit<-lmFit(eset,design) >colnames(design) <- c("CTR","DIS") >cont.matrix<-makeContrasts(DISvsCTR=DIS-CTR,levels=design) >fit<-contrasts.fit(fit,cont.matrix) # here I am getting the warning message: #In contrasts.fit(fit, cont.matrix) : row names of contrasts don't match col names of coefficients. I guess this is because in my eset has 1st column row names. How do I accomodate that? Thanks, Viritha [[alternative HTML version deleted]]

Hi group, I just got to know the error. I am giving the colnames(design) after lmFit(eset,design). If I interchange this.It works fine. Thanks, Viritha On Thu, Apr 14, 2011 at 2:01 PM, viritha kaza <viritha.k@gmail.com> wrote: > Hi group, > I have a patient dataset of 6 control and 11 disease. > so the code that I have written is: > > >library(affy) > >library(limma) > >eset<-as.matrix(read.table("GSEXXXX_series_matrix.txt",header = TRUE,sep = > "\t", row.names = 1, as.is = TRUE) > > design <- model.matrix(~-1 + > factor(c(1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2))) > > fit<-lmFit(eset,design) > >colnames(design) <- c("CTR","DIS") > >cont.matrix<-makeContrasts(DISvsCTR=DIS-CTR,levels=design) > >fit<-contrasts.fit(fit,cont.matrix) > > # here I am getting the warning message: > #In contrasts.fit(fit, cont.matrix) : row names of contrasts don't match > col names of coefficients. > > I guess this is because in my eset has 1st column row names. > How do I accomodate that? > Thanks, > Viritha > > > [[alternative HTML version deleted]]