[BioC] edgeR/DESeq for ChIP-seq analysis

[Cittaro Davide]

Dear Mark

On Nov 8, 2012, at 8:53 AM, Mark Robinson <mark.robinson at imls.uzh.ch> wrote:

> Dear Davide,
> 
> Indeed, edgeR and DESeq can be (and have been) used in this mode.  We published something recently on this:
> 
> http://www.ncbi.nlm.nih.gov/pubmed/22879430
> http://imlspenticton.uzh.ch/robinson_lab/ABCD-DNA/ABCD-DNA.pdf
> 

I've missed that :-( Thanks for the paper

> You can apply that approach regardless of copy number being a factor ... basically, we counted tiled bins of the genome, but yes, you could focus in on regions of interest.  The function abcdDNA() is really just a wrapper for the edgeR GLM.  As usual, "normalization" can be delicate, depending on the type of data.
> 
> Also note that the DiffBind package already does something similar, but has a lot more machinery to collect and organize the sets of enriched regions.

I wonder why I've never used DiffBind before :-)

> 
> Hope that helps.

It does, thanks!

d

> 
> Best, Mark
> 
> 
> On 08.11.2012, at 08:37, Cittaro Davide wrote:
> 
>> Hi there, I'm writing to the list to have your comment about the possibility of using edgeR or DESeq for the analysis of ChIP-seq samples.
>> Standard approaches to ChIP-seq analysis (relying on external software such as MACS) do not make analysis of replicates easy. I've seen people looking for peaks and then compare the common/differential intervals between replicates in case/control design. I wonder if a more general approach may work (and I'm going to test this anyway...).
>> Since the negative binomial model stands for ChIP-seq analysis, both edgeR and DESeq should work well. One can use external software to identify regions and compute the union of all regions as it was a "gene list". From that point on, the pipeline should not differ from standard gene expression analysis.
>> What do you think?
>> 
>> d
>> /*
>> Davide Cittaro, PhD
>> 
>> Coordinator of Bioinformatics Core
>> Center for Translational Genomics and Bioinformatics
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>> Via Olgettina 58
>> 20132 Milano
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>> Office: +39 02 26439140
>> Mail: cittaro.davide at hsr.it
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> Bioinformatics
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/*
Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
Ospedale San Raffaele
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cittaro.davide at hsr.it
Skype: daweonline
*/