>From your description it seems that your arrays have different numbers of spots as well as different layouts. limma does not have facilities for simultaneous analysis of arrays of different sizes. You need to analyse the arrays separately. Or perhaps you might be able to align the different arrays after averaging over the within-array replicates. There aren't any functions available to do this for you automatically. Gordon > Date: Wed, 25 May 2005 19:20:24 -0400 (EDT) > From: "NATALIA F TCHETCHERINA" <nxt7@psu.edu> > Subject: [BioC] global normalization > To: bioconductor@stat.math.ethz.ch > > > > Hello all, > I have question about global normalization. > I have data from big experement(two-color cDNA arrays) where used three > different layouts but the same set of genes. > I used limma package for within array normalization. > My question is: how I can do between array normalization (global) if arrays have > different layout(different location and different number technical replicates > (number of spots of a gene on an array))? > > Sincerely, Natalia.