Hello, If this has been discussed in the archives, my apologies but I couldn't find it. I am comparing two array CGH datasets, one generated by Nimblegen and a two color 70mer array I have genepix .gpr files for. I've been learning limma and everything works fine but I want to do the normalization the same way as Nimblegen. I believe they use the normalize.qspline from the affy package and so I believe they analyze the channels separately. I wanted to know if the robust spline function in limma is equivalent (or close enough) to the qspline implementation from the affy package? There are many references to different spline functions in the help and wondered if anyone could shed a little light on what will work given that I'm starting from .gpr files... Thank you for your time. Sincerely, Betty Gilbert -- Betty Gilbert lgilbert at berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720