[Bioc-devel] eSet class and two color arrays

[Wolfgang Huber]

Hi Seth, Sean

> So the use case is that one wants to subset all phenoData and
> assayData components simultaneously?
> 
> I want to understand what features are desired beyond those provided
> by a list of ExpressionSet instances (at first glance, a list seems
> quite close to what you are asking for).

More than a list:
- simultaneous subsetting
- consistency of dimensions and their content


Sean Davis wrote:
> I think the point Wolfgang is trying to make (feel free to clarify,
> Wolfgang) is that the current phenoData and assayData constructs are
> "Array-centric" while biologic questions can be asked that are
> "sample-centric".  In other words, one often wants to treat
> the two channels > on a single array as "separate samples" in a sense
> (of course linked to each  other by array).

Yes. An easy way out is to switch completely from array-centric to
sample-centric (that's e.g. what arrayMagic does), but really one often
wants to have both.

Of course this whole discussion is not about what is possible to do
(everything is possible with R) but how convenient it is.

 Cheers W.



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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber