[BioC] Rat Nimblegen promoter dataset HOWTO

[Tobias Straub]

I suggest that - after array normalization (i recommend vsn) - you  
apply common statistics used for differential gene expression (e.g.  
moderated t-statistics) on a probe level (control vs. treatment). for  
the t-statistics you should only look at probes that are - within the  
arrays of an experimental group - significantly enriched for your  
histone modification before or after treatment. you then can e.g. set  
a threshold (fdr-based) and define significantly changed probes.  
afterwards you combine adjacent significantly changed probes using  
either a sliding window or a hidden markov model as on tiling arrays  
you have to assume that more than single probes will respond due to  
the chromatin resolution that spans more than one probe.

that will reveal changed regions that - hopefully - locate where you  
hope ;-) on promoters.
sounds complicated but shold be fairly easy.. if you are a bit  
familiar with R!
best
T

On Jan 17, 2008, at 4:59 PM, Dario Greco wrote:

> 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
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> email: dario.greco at helsinki.fi
>
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======================================================================
Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany