[BioC] ChIP-Seq Normalization - Quantile (Rank) normalization

[Wei Shi]

Hi Henry:

	There are a few BioC packages which can perform quantile normalization. One of them is the normalizeQuantiles function in limma. 

Cheers,
Wei



On May 10, 2011, at 12:15 AM, Henry Paik wrote:

> Hello BioC,
> 
> I am wondering if there is a package or example codes to quantile-normalize ChIP-Seq data.
> 
> I would like to compare Sample vs. Sample and think it would be nice to use quantile normalization - sort of we use it for microarray.
> 
> I looked up a couple of tools - MACS and QuEST. It seems that they normalize by "scaling linearly."
> 
> Sequencing and microarray do not share the exact features but for normalization, wouldn't it be okay to use quantile normalization?
> 
> Thanks!
> 
> - Henry
> 
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