Hi Dario,

Try ChIPper (Gibbons,FD. 2005.Genome Biol 6,R96; http://llama.med.harvard.edu/software.html). You can download the R code from the web site. It is not a Bioconductor/R package, so you may have to modify the code a little in order to make it work.

Kind regards,
Juerg


-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Dario Greco
Sent: Thu 1/17/2008 10:59 AM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] Rat Nimblegen promoter dataset HOWTO
 
Dear List,

I am going to analyze a set of Rattus Norvegicus Nimblegen promoter arrays.
briefly, i have 6 slides. in each slide, the ChIP (of a Histon) and the 
input chromatin have been hybridized.
of these 6 slides, 3 are from control animals, and 3 from animals 
treated with a specific drug.

i am interested in finding promoters differently enriched in treated vs 
control animals.

i have not very clear ideas about the steps/BioC-tools of this kind of 
analysis, so any help is very welcome.

thank you very much,
yours
d

-- 
Dario Greco
MSc, PhD student
Institute of Biotechnology - University of Helsinki
Building Cultivator II, room 223b
P.O.Box 56    Viikinkaari 4
FIN-00014    Finland
Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780
email: dario.greco@helsinki.fi

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