[Bioc-devel] RFC: eSet with two color data

Wolfgang Huber huber at ebi.ac.uk
Mon Mar 26 16:26:12 CEST 2007

Hi Seth,

> Thinking through option A, it also requires infrastructure because it
> breaks the subsetting model in the other direction.  If a user does:
>     x[1:3, ]
> what should happen? With the current code, they would get something
> that would not be a valid n-colour set and probably would not be
> desired in this context.  Since both options require some subset
> coding, I think going for the option that suggests more efficiency
> is best.

What should happen is that they get an ExpressionSet with only three
features, but the same samples (arrays x colours = columns of exprs and
rows of phenoData). The different colours are stored sideways, so unless
I really need to catch up with recent changes in Expression specs, I
think the row-subsetting does what we want.

Best wishes

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

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