[BioC] help in 2-color data normalization

[Jianping Jin]

Dear list,

I used r/gPreProcessedSignals from Agilent FE outpup files as a start to 
analyze without any filtering. The density plot (see attachment) indicates 
that both channels were pretty well consistent in high intensity range. 
There were separate read and green peaks, however, which located at log2 
(5) and log2 (4) respectively. MA plots were pretty normal (see attached).

The experiment was human colon cancer versus Stratgen universal human 
cancer RNAs. These two minor peaks, to me, may be more than what could be 
explained by just dye bias. As r/gPreprocessedSignal is supposed to have 
gone through a lowess normalization or something like that. Could they be 
"real" difference between the samples and the universal reference?

Has anyone had similar observations? I appreciate any comments to help me 
out?



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu