Two-channel (color) microarrays are usually normalized with LOESS, but one-channel arrays usually only with a between-array method (like quantile). The best tool to use is limma, you can read in the manual how to normalize and analyze these different array types, including case studies with scripting codes.
As per Benn:
in the limma, it has two different part of two color, one is direct two-color, do you know the meanning
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