Message-ID: <m2mzcva6n1.fsf@ziti.local>
Date: 2006-06-02T16:01:38Z
From: Seth Falcon
Subject: [Bioc-devel] eSet class and two color arrays
In-Reply-To: <44803548.9050602@ebi.ac.uk> (Wolfgang Huber's message of "Fri, 02 Jun 2006 13:55:36 +0100")
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).
+ seth