[Bioc-devel] eSet class and two color arrays
Wolfgang Huber <huber at ebi.ac.uk> writes:
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).
Thanks. That along with some offline conversations give me a much clearer picture of what is needed here.
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.
I don't disagree that reusing code is a good goal, but as Robert explained, the eSet class is intended for processed, not raw, data. I think a good approach would be for an interested party to consider building a rawSet class that made use of some of the same component objects as eSet (AnnotatedDataFrame and AssayData). I'm pretty sure one does not want a subclass of eSet because the behaviors one will want, even in terms of subsetting, I think are quite different. + seth