I have used SCAN.UPC for Affy and it worked better in comparison to other normalization methods. I would like to implement the same for Illumina and Agilent single channel arrays. Is it possible to perform?? If so, how to proceed with that??

I'm glad you like the tool. It is possible to apply the UPC method to data from these microarray types. But we don't yet have SCAN working for them. I am hoping to get this implemented at least for Agilent single-channel arrays by the next release.