Hi,

I would like to analyze some agilent aCGH copy number files. As a start, I
would like to normalize this data. I don't know what is the standard way to
do this. Which package is the standard one that people use for this
purpose? The chips that I am looking at are the agilent sure print 1M
(G4447a) array and a custom chip with similar format. My raw data is a text
file with spot locations and intensities. It is a two color array.

Thanks for your help!

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