[BioC] quantile normalization approach

[Rafael A. Irizarry]

On Sat, 22 Mar 2003, Wang, Hui wrote:

> Hi List,
> 
>  
> 
> Quantile-quantile normalization assumes common distribution for data sets to
> be normalized. I am fine with replicate normalization using this. However,
> for different experiments, such as data from different tissues, is the
> assumption still valid?

probably not. but when replicate arrays have completely
different distributions, in my opinion one is left with with no choice but
to make such assumaptions. are you willing to make the assumption they all
have the same median? how about the same quartiles? where to draw the line
is not easy.

> 
>  
> 
> Could anybody point me to some reference that conducts comparison under many
> different experimental conditions? (for example, under >10 different tissues
> or cell line experiments).  I read all the papers/ documents I can find. But
> still not convinced we can use that assumption.
> 
>  

both RMA papers (Biostatistics and NAR) apply the method to the diltion
data set that has liver and central nervous system cell lines.


> 
> Thanks
> 
>  
> 
> Regards
> 
> -h
> 
> 
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> 
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