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

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Wed Oct 11 20:06:56 CEST 2006

> > 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.

Hi Sean

Rafa and Benilton directed me to their TilingFeatureSet class which
will cover the tiling case.  As you note the Harbison example is
different and I do not want to steal the ChIPset name for this
possibly outmoded approach.  maybe nonTilingChIPset?  I don't know
how many exemplars we may want to have of this kind of data, so I don't
want to sweat it too much.

If no one anticipates multiple exemplars of this kind of data, we
could just use ExpressionSet and live with the terminologic abuse.


> Sean

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