[BioC] RMA normalization

[Hairong Wei]

I just started to work on low-level microarray data analysis and do not have
experience in using RMA algorithm.   I am now in a situation where I have to
normalize a a few hundred of arrays across multiple tissues.   I have seen a
few messages regarding the legitimacy of using quantile-quantile (Q-Q)
method to normalize many arrays across multiple tissue types in the
bioconductor archive.   It seems that normalization within tissue-of-origin
was favored by some folks.  Although I feel it is the approach I should
take, I still hope to be more secure before I do it, just bacuse a lot of
work will be done on the normalized data.  

Can anybody help by pointing out a few references that use Q-Q method within
or not within tissue-of-origin?   For those who has done Q-Q within the
tissue-of-origin, could you please give some comments or your feelings
regarding Q-Q withn tissue-of-origin?

Hairong    

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