[BioC] Rat Nimblegen promoter dataset HOWTO

Joern Toedling toedling at ebi.ac.uk
Thu Jan 17 17:24:59 CET 2008

Hi Dario,

depending on the type of arrays you have, the Bioconductor packages
Ringo and oligo may be of interest to you. Please have a look at their
I guess you mean that in your ChIP an antibody against a histone tail
modification has been used. We have created and used the package Ringo,
which relies on limma, for such an analysis, but there are also a number
of other valuable approaches available through Bioconductor, for example

Hope this helps to get you started,

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

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