Hi, I have a question about the function avereps in the limma package. When I compare the relative outputs of this function in limma.2.18.2 and in the last version limma.3.6.6, I find different results. If we take for example a gene with two probes : - probe1$M = 2 - probe2$M = NA The results will be : - for limma.2.18.2 : 2 - for limma.3.6.6 : 1 The codes are : - for limma.2.18.2 : for (i in 1:length(u)) y[i,] <- colMeans(x[ID==u[i],,drop=FALSE],na.rm=TRUE) - for limma.3.6.6 : rowsum(x,ID,reorder=FALSE,na.rm=TRUE)/as.vector(table(ID)) So : - for limma.2.18.2 : colMeans(as.matrix(c(2,NA)),na.rm=TRUE) [1] 2 - for limma.3.6.6 : (2 + 0) / 2 = 1 rowsum(as.matrix(c(2,NA)),c(1,1),na.rm=TRUE)/as.vector(table(c(1,1))) [,1] 1 1 For me, NA don't mean 0, so do you agree with me ? Cheers Gildas