[BioC] Rat Nimblegen promoter dataset HOWTO
Tobias Straub
tstraub at med.uni-muenchen.de
Thu Jan 17 18:28:38 CET 2008
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
> Fax: +358 9 191 58952
> Mobile: +358 44 023 5780
> 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
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