Hi, I am working on 2x2 Factorial Experiment(ANOVA With interaction factor)and following Limma user guide( chapter 11.4 Estrogen Data). Basically I am interested in knowing how ?gender? variable is effecting outcome of experiment(please see attached file for sample information) is effecting But I am getting error at ?colnames(design)? *Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent* * * *This is list of R codes that I ran for getting to this point * ? targets <- readTargets("phenoData.txt",sep=",",row.names="filename") ? contrasts(treatments) <- cbind(Type=c(0,0,0,0,1,1),MMut=c(0,1,0,0,0,0),FWT=c(0,0,1,0,0,0),MWT =c(1,0,0,0,0,0),FMut=c(0,0,0,1,0,0),NonTgM=c(0,0,0,0,0,1),NonTgF=c(0,0 ,0,0,1,0)) ? > contrasts(treatments) ? Gender MMut FWT MWT FMut ? MMut 0 0 0 1 0 ? MWT 0 1 0 0 0 ? FMut 0 0 1 0 0 ? FWT 0 0 0 0 1 ? NonTGM 1 0 0 0 0 ? NonTGF 1 0 0 0 0 > design <- model. Matrix(~treatments) > design (Intercept) treatments Type treatmentsMMut treatmentsFWT treatmentsMWT treatmentsFMut 1 1 0 0 0 1 0 2 1 0 0 0 1 0 3 1 0 0 0 1 0 4 1 0 0 0 1 0 5 1 0 1 0 0 0 6 1 0 1 0 0 0 7 1 0 1 0 0 0 8 1 0 1 0 0 0 9 1 0 0 1 0 0 10 1 0 0 1 0 0 11 1 0 0 1 0 0 12 1 0 0 1 0 0 13 1 0 0 0 0 1 14 1 0 0 0 0 1 15 1 0 0 0 0 1 16 1 0 0 0 0 1 17 1 1 0 0 0 0 18 1 1 0 0 0 0 19 1 1 0 0 0 0 20 1 1 0 0 0 0 21 1 1 0 0 0 0 22 1 1 0 0 0 0 23 1 1 0 0 0 0 24 1 1 0 0 0 0 Any help is greatly appreciated. Ash -------------- next part -------------- Type Filename Gender 1Mut-F1 1Mut-F1.CEL F 1Mut-F3 1Mut-F3.CEL F 1Mut-M4 1Mut-M4.CEL M 1Mut-M5 1Mut-M5.CEL M 6 WT-F2 6 WT-F2.CEL F 6 WT-F3 6 WT-F3.CEL F 6 WT- M2 6 WT- M2.CEL M 6 WT - M3 6 WT - M3.CEL M 24 WT-F4 24 WT-F4.CEL F 24 WT-M3 24 WT-M3.CEL M 24 WT-M4 24 WT-M4.CEL M 101Mut -F1 101Mut -F1.CEL F 101Mut -F2 101Mut -F2.CEL F 101Mut -M1 101Mut -M1.CEL M 101Mut-M2 101Mut-M2.CEL M Non-Tg-M1 Non-Tg-M1.CEL M Non-Tg-M2 "Non-Tg-M2,CEL" M Non-Tg-F2 Non-Tg-F2.CEL F Non-Tg-F3 Non-Tg-F3.CEL F