Hi friends, I would like to carry out a similar analysis of data to which carries out affylmGUI, but with standard sign data with MAS5, and to carry out a statistical eBayes to the carried out contrast the same as in affylmGUI. Serious this correct? I have tried to carry out it but I find that the data that I obtain are not correct or distance much of the analysis that I have carried out with GCRMA in affylmGUI. These are my chips: pData(eset) sample mtl1-diam.CEL 1 mtl1-diam2.CEL 2 mtl1.2.CEL 3 mtl1.CEL 4 wt-diam2.CEL 5 wt-diam3.CEL 6 wt2.CEL 7 wt3.CEL 8 I have two you reply of each condition. And I want to carry out the following contrasts: mtl1 vs wt mtl1.diam vs mtl1 wt.diam vs wt This is the script that I have used for the analysis, noticing limma user's guide. >eset<-call.exprs(data,"mas5") >strain = c("mtl1.diam","mtl1.diam","mtl1","mtl1","wt","wt","wt.diam","wt.diam") >design = model.matrix(~factor(strain)) >colnames(design) = c("mtl1.diam","mtl1","wt","wt.diam") >fit<-lmFit(eset,design) >contrast.matrix<-makeContrasts(mtl1-wt,mtl1.diam-mtl1,wt.diam-wt, levels=design) >fit2<-contrasts.fit(fit,contrast.matrix) >fit2<-eBayes(fit2) >results<-decideTests(fit2) Not you if there is something in the design of the analysis that I make bad. I thank all their help. Thank you ********************************* Pedro Bot?as Talamantes Unidad de Gen?mica Parque Cient?fico de Madrid-UCM Facultad CC Biol?gicas- Planta s?tano Universidad Complutense de Madrid 28040 Madrid Tel: 91 3945036 FAX 91 3944883 e-mail: pbotias at bio.ucm.es Web: http://www.ucm.es/info/gyp/genomica/