Hi I have to say the limma userguide is now one of the most comprehensive guides available for microarray analysis. It is therefore regretfully that I ask for additional information... The guide rightly points out that we must not treat arrays that are technical replicates as true replicate arrays as they are not independent. Sections 10.1 and 10.2 then go on to explain how technical replicates can be handled using either duplicateCorrelation or by manipulating the contrasts matrix. However, both these examples deal with arrays where direct comparisons have been made. I have data from a common reference design, comparing two groups using a common reference, with biological replicates and technical replicates (dye swaps) and it's not immediately clear from the examples how I should deal with the technical replication. Many thanks for any hints forthcoming! Mick