[Bioc-devel] eSet class and two color arrays

[Sean Davis]

On 6/2/06 12:01 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> Wolfgang Huber <huber at ebi.ac.uk> writes:
> 
>> sorry, I used inexact language in the previous mail: of course there is
>> always exactly one assayData slot, but that may contain one or several
>> matrices of equal dimensions.
> 
> :-)
> 
>>> one of the basic features of the eSet class is that
>>> - it has exactly one phenoData slot, and >=1 assayData slots
>>> - the rows of the dataframe in phenoData correspond 1:1 to the columns
>>>   of each the assayData matrices.
>>> 
>>> I was wondering whether there is interest in a class that has
>>> - one or several phenoData slots, and the same number of assayData slots
>>> - there is a 1:1 correspondence between these
>>> - the rows of each phenoData correspond to the columns
>>>   of the corresponding assayData matrix.
>>> 
>>> Andreas Buness from arrayMagic has a use case where such a class could
>>> be used to represent raw two-color microarray data.
> 
> 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).

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.  

Sean