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

[Alicia Oshlack]

Hi Henry,

In my view it's not obvious how you would perform quantile normalization on ChIP-seq data. Were you planning to bin the data then quantile normalize binned counts? Then you run into the issue of what bin size to use for all you analysis and most peak-finding programs will not take binned data. Even if you use each base as a bin we know there are base specific biases so it's not clear that this would be effective especially as there will be very many 0 and 1 counts.

Cheers,
Alicia
 

Date: Tue, 10 May 2011 09:13:18 +1000

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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