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

[Henry Paik]

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