Hi, I am using limma. Here is a error I met SubM is a 19k by 6 matrix > design [1] 1 1 1 -1 -1 -1 > PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation=mycor$cor,weig hts=NULL) > PMAfit<-ebayes(PMAfit) > topT<-toptable(PMAfit,number=200,sort.by="P",genelist=genelist,adjust= "fdr") Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), : attempt to set an attribute on NULL Thanks

Try using eBayes() instead of ebayes() and topTable() instead of toptable(), ie PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation=mycor$cor,weig hts=NULL) PMAfit<-eBayes(PMAfit) topT<-topTable(PMAfit,number=200,sort.by="P",genelist=genelist,adjust= "fdr") Also be sure that your genelist is the right size (half as many rows as the original gal file, since you have averaged over the duplicate spots in the linear model fit). The function uniquegenelist() will do this for you. Best wishes, Matt Ritchie > Hi, > I am using limma. Here is a error I met > > SubM is a 19k by 6 matrix > > design > [1] 1 1 1 -1 -1 -1 > > > PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation=mycor$cor,we ights=NULL) > > PMAfit<-ebayes(PMAfit) > > > topT<-toptable(PMAfit,number=200,sort.by="P",genelist=genelist,adjus t="fdr") > Error in array(x, c(length(x), 1), if (!is.null(names(x))) > list(names(x), : > attempt to set an attribute on NULL > > Thanks