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

Seth Falcon sfalcon at fhcrc.org
Mon Mar 26 17:02:26 CEST 2007

Wolfgang Huber <huber at ebi.ac.uk> writes:

> 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.

Sorry, not enough coffee for me yet.  Yes, row-subsetting does what we
want I think.  What I'm concerned about is column-subsetting:

    x[, 1:3]

The result is no longer an n-colour set and this breaks the "["
concept.  With option A you want certain code to be able to assume
that the structure of the exprs matrix is ncol = arrays * colours.
Without some coding effort, you cannot have this work in a general

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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