[Bioc-devel] Couple of eSet questions

Robert Gentleman rgentlem at fhcrc.org
Mon Feb 6 16:55:58 CET 2006

Sean Davis wrote:
> On 2/3/06 4:05 PM, "Vincent Carey 525-2265" <stvjc at channing.harvard.edu>
> wrote:
>>>>eSet itself does not need to solve the two channel or
>>>>error-available problems at once.  it should be extended to do so,
>>>>with explicit use cases stated.
>>>Yes, I'm just not convinced that eSet has any business having actual
>>>data slots; those are the domain of its subclasses.
> I'm just curious as to when and by whom eSets will be subclassed?  Will that
> be left to individual package developers, or will these subclasses be
> available in biobase for general consumption?

  Ideally there would be platform/experimentt specific subclasses. 
Initially I would expect them all to be different, but overtime for 
consensus to appear. For example, we would be really supportive of some 
move on the arrayCGH front that went for a standardized data format (and 
some form of eSet could be used). For flow cytometry the prada package 
has already done something along these lines and we make some use of it 
in rflowcyt.

   I doubt it would all go in Biobase, but rather that there might be a 
aCGHBase and a flowBase etc that would help to accommodate different groups.

   Whether that happens depends a lot on those folks. We try pretty hard 
not to enforce any particular style but rather to show that there are 
benefits from using common formats and to having the data be as 
self-describing as possible.

Hopefully, once we make some progress on the microarray experiment 
repository more people will see the benefits of this approach, but maybe 

  best wishes

> Sean
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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