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

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Wed Oct 11 18:53:01 CEST 2006

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

any concerns with this plan?  any other formats for proprietary
ChIP-chip data that I don't know about but should?


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