[Bioc-devel] eSet for aCGH data

Sean Davis sdavis2 at mail.nih.gov
Thu Oct 4 13:45:58 CEST 2007

Vosse, S.J. wrote:
> Dear all,
> first let me thank Martin Morgan and James MacDonald for their answers
> to my question about the exprSet class on the Bioconductor mailing list.
> They have been very helpful.
> I am thinking to adapt/extend the eSet class or probably ExpressionSet
> to contain aCGH data for our package CGHcall. My question is whether a
> similar class for aCGH data already exists or if anyone has been working
> on it or has thoughts on the subject. The class would be the same as
> ExpressionSet, only there would need to be slots for raw data,
> normalized data, segmented data, called data and regions data
> (http://la-press.com/cr_data/files/f_CIN-3-Wiel-et-al_96.pdf).

If I were going to do this, I would think about separate subclasses for 
raw data, normalized data, and segmented data.  If you think about 
methods for each class, you will probably want them to behave 
differently based on whether they are operating on raw, normalized, or 
segmented data.  Having separate subclasses makes this pretty 
straightforward.  Just a thought, though.


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