Respected Mam/Sir,, I would like to know about design matrix and contrast, I have four CEL files, two from wild type and two from mutant, each have two repliates. I normalized the data,, I have expression value in *dat.m*. Now I consider differential expression fit<-lmFit(dat.m, design) fit<-eBayes(fit) topTable(fit, coef=2) tt<-toptable(fit, coef=2, n=nrow(dat.m)) rn<-rownames(tt)[tt$P.Value<-0.001] I got only 127 genes But i dont know how to work limma package, In my folder have four CEL files. How to limma know about wild type and mutant cel files and how compare, that i want to know ? In above commands am not mention about cel files, which file is belong to wild type & other.. How this package do work for 4 cel files??? Thanks & Regards Varpall [[alternative HTML version deleted]]

Hi Varpal, varpal singh wrote: > Respected Mam/Sir,, > > I would like to know about design matrix and contrast, I have four CEL > files, two from wild type and two from mutant, each have two repliates. I > normalized the data,, I have expression value in *dat.m*. > Now I consider differential expression > > fit<-lmFit(dat.m, design) > fit<-eBayes(fit) > topTable(fit, coef=2) > tt<-toptable(fit, coef=2, n=nrow(dat.m)) > rn<-rownames(tt)[tt$P.Value<-0.001] > I got only 127 genes > > But i dont know how to work limma package, In my folder have four CEL files. > How to limma know about wild type and mutant cel files and how compare, that > i want to know ? > In above commands am not mention about cel files, which file is belong to > wild type & other.. I think the Limma User's Guide covers this quite extensively. You can read it using limmaUsersGuide() Best, Jim > > How this package do work for 4 cel files??? > > Thanks & Regards > Varpall > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues