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

[Vincent Carey 525-2265]

> > 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.

Thanks

> Sean
>