[Bioc-devel] RFC for a container for ChIP-chip data

[Sean Davis]

On Wednesday 11 October 2006 12:53, Vincent Carey 525-2265 wrote:
> I am working on an experimental data package for the Harbison
> (PMID 15343339) yeast regulatory code paper.
>
> the assay data can be looked at either in a gene-centric way (e.g.,
> reporters are genes; most convenient, but some ambiguity) or more
> literally using the intergenic region, for which we have sequence
> information.  the intergenic regions are the things that are
> actually spotted.
>
> my plan at the moment -- define a ChIPset class that extends
> eSet; the AssayData will probably have accessor brats (for
> binding ratios, not exprs), and i will try to set up featureData
> to have some information on associated intergenic region for
> a gene-centric representation of the assay.  The phenoData will
> give information on the TFs that were chipped for each AssayData
> column
>
> any concerns with this plan?  any other formats for proprietary
> ChIP-chip data that I don't know about but should?

Vince,

This looks good for non-tiling Chip-chip data, but not for tiling or 
promoter-tiling chips which are rapidly becoming the standard (?) for 
performing chip-chip analysis.  I would vote for making some distinction 
between gene-based chip-chip data and tiling/promoter-based chip, as the 
analysis methods and featureData are quite distinct from PCR-product based 
arrays.  This is probably just a naming thing, but I think ChIPset implies 
different things to different people.  Or, if you go with ChIPset, I guess a 
TilingChIPset could be created?  I'm not proposing a solution, but just 
pointing out that to many people, ChIP-chip data will imply tiling-array data 
with genomic locations, etc. and to others it will not.

Sean