[BioC] ChIP-Seq Normalization - Quantile (Rank) normalization
Wei Shi
shi at wehi.EDU.AU
Tue May 10 01:13:18 CEST 2011
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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}
More information about the Bioconductor
mailing list