[Bioc-devel] eSet class and two color arrays

Seth Falcon sfalcon at fhcrc.org
Fri Jun 2 19:05:29 CEST 2006

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
       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 :-)


+ seth

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