[BioC] help in 2-color data normalization

[Jianping Jin]

Sorry I made some mistakes on attachment of plots in my last email. I sent 
it again therefore. Sorry for multiple versions of emails.

Dear list,

I used r/gPreProcessedSignals from Agilent FE outpup files as a start to 
analyze without filtering out any genes, except for those control spots. 
The density plot indicates that both channels were pretty well matched 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 (please visit the site for viewing plots: 
<http://www.unc.edu/~jjin/Graph/> )

The experiment was human colon cancer versus Stratgen universal human 
cancer RNAs. The two minor peaks, to me, may be more than what could be 
explained by just dye bias. As r/gPreprocessedSignal was 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?

thanks,

Jianping

##################################
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