Hi, I am trying to analyze gene expression data from some customized single channel arrays having only 40 genes including control probes. I have enough replicates to work with. Can anybody suggest a method for background correction and normalization for these kind of arrays? I have around 8 slides.Even links to references would be highly appreciated. Thanks, Som.

The limma package provides a range of background and normalization options, some of which make use of control probes.