[BioC] ChIP on Chip normalization

[Wolfgang Huber]

Hi Ido,

> has anybody experience with Chromatin IP on Chip normalizations?
> We use an oligo tiling array as well as a ~500bp DNA fragments 
> spotted array (which is my priority currently). 
> 
> Are there special normalization procedures in some of the packages?
> I couldn't find any of those yet.

Normalization always needs to be adapted to the particular platform,
quality issues etc. of the arrays at hand, but why do you think you need
a special normalization procedure for ChIP compared to RNA hybridization?

We have successfully used vsn (in the package of the same name) for
normalizing ChIP data on two-color  spotted arrays, and I know other
people have used loess-normalization (marray or limma packages) as well.
-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber