[Bioc-devel] eSet class and two color arrays

[Seth Falcon]

Wolfgang Huber <huber at ebi.ac.uk> writes:
> More than a list:
> - simultaneous subsetting
> - consistency of dimensions and their content

Got it.

> 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).  Currently, one can't get at
> the information associated with a single sample (or channel) easily,
> only the information for a single array.

Here's my mental model (please help me improve it ;-):

   You have a collection of samples and for each sample you have a
   foreground and a background measurement each in two different
   colors (say red and green for discussion).

   So would think you'd want an assayData slot containing four
   matrices:
       
       Rb  Red background
       Rf  Red foreground
       Gb  Green background
       Gf  Green foreground

   Each matrix has dim genes (rows) by samples (coloumns).  A column
   in any of these matrices refers to the same biological sample and
   corresponds to a single row in phenoData.

I'm guessing the above described structure is not sufficient, but
I don't yet understand why.  

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

Or what "it" is :-)

Best,

+ seth