[Bioc-devel] eSet class and two color arrays

[Wolfgang Huber]

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



Wolfgang Huber wrote:
> Hi Martin, Seth, & others,
> 
> 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.
> 
> Alternatively, it is also possible to put two-color data into the
> existing eSet design, if a convention is used that each array is
> represented by two rows in phenoData (corresponding to the two colors)
> and two columns in assayData. This is essentially what now happens in
> the exprSetRG class of arrayMagic. So a useful eSet-based class for
> two-color data (formalizing the convention) could still be derived from
> the existing eSet definition. But I wanted to put up this for
> discussion: do other people have a need/wish for "multiple phenoData"
> design?
> 
> Cheers
>  Wolfgang
>