[BioC] RMA normalization

[Adaikalavan Ramasamy]

What do you mean by "normalization within tissue-of-origin" ? Can you
give us examples of these messages/papers/references discussing this.

I often work with finding differentially expressed genes between two
phenotypes of the same type of cancer and tissue type. How would this
normalisation work then ?

Regards, Adai



On Thu, 2004-09-09 at 16:43, Hairong Wei wrote:
> 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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