[Bioc-devel] eSet class and two color arrays

[Wolfgang Huber]

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

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