Hi All, In my analysis, I want to find the different expression genes between dissese A and B. There are two type of batch effect in my analysis. I want to use limma to remove two type of batch effect, one is gender, another is tissue type. I do as fellow. But I got a error. Is there some problem in my analysis? Thank you very much in advance. design<-model.matrix(~0+factor(pData(mldat.norm)$AvsB)+factor(pData(ml dat.norm)$gender)+factor(pBatch)) colnames(design) <- c("group1","group2","Sexbatch","pBatch") fit1 <- lmFit(exprs(mldat.norm),design) Coefficients not estimable: pBatch Warning message: Partial NA coefficients for 29198 probe(s) contrast.matrix <- makeContrasts(group2-group1,levels=design) fit2 <- contrasts.fit(fit1, contrast.matrix) fit2 <- eBayes(fit2) topTable(fit2, coef=1,adjust="BH",sort.by="P")

wouldn't it help to do design <- model.matrix( ~ 0 + factor(AvsB) + factor(gender) + factor(pBatch), data=pData(mldat.norm)) and then carry on? It looks like you're trying to reference something that ain't defined On Tue, Dec 28, 2010 at 4:21 AM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote: > Hi All, > > In my analysis, I want to find the different expression genes between > dissese A and B. There are two type of batch effect in my analysis. I > want to use limma to remove two type of batch effect, one is gender, > another is tissue type. I do as fellow. But I got a error. Is there > some problem in my analysis? Thank you very much in advance. > > > design<-model.matrix(~0+factor(pData(mldat.norm)$AvsB)+factor(pData( mldat.norm)$gender)+factor(pBatch)) > colnames(design) <- c("group1","group2","Sexbatch","pBatch") > > fit1 <- lmFit(exprs(mldat.norm),design) > Coefficients not estimable: pBatch > Warning message: > Partial NA coefficients for 29198 probe(s) > > contrast.matrix <- makeContrasts(group2-group1,levels=design) > fit2 <- contrasts.fit(fit1, contrast.matrix) > fit2 <- eBayes(fit2) > topTable(fit2, coef=1,adjust="BH",sort.by="P") > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]