Hello, I have an experiment where there are some Nimblegen 2.1 million probe Mouse promoter arrays with IPs always in the red channel and input DNA always in the green channel. I notice that the arrays have some probes of type Random, which I assume should not be changing between channels. So, I'd like to use normalizeWithinArrays with method = "control". I call the method as : normalizeWithinArrays(RG, method = "control", controlspots = RG$genes$Status == "Random") and get the error : Error in normalizeWithinArrays(RG, method = "control", controlspots = RG$genes$Status == : Layout argument not specified I'm confused as to why it requires the layout ? I didn't think newer array designs had print tip groups or replicate spots ? -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia