[Bioc-devel] eSet class and two color arrays

Wolfgang Huber huber at ebi.ac.uk
Fri Jun 2 19:37:47 CEST 2006

Hi Seth,

> 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
>    matrices:
>        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.

No, different samples are on the red and green channels (so these four
matrices correspond to two phenoData object rows).

One way to close this thread is Robert's answer, and I do not object.

(Still it sticks that "raw" data is not always that different from
"processed" data, whereever you draw the line, and reusing what is there
as much as possible could, in an ideal world, where people care, be
better than making up, maintaining and making people learn completely
different data structures. AffyBatch/exprSet is an example where that
worked, even though arguably the difference between GeneChip "raw" data
and processed is not smaller than between two-color raw data and processed.)

Best wishes

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

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