Message-ID: <m2ps6wvyil.fsf@ziti.fhcrc.org>
Date: 2007-03-26T15:02:26Z
From: Seth Falcon
Subject: [Bioc-devel] RFC: eSet with two color data
In-Reply-To: <4607D804.4090306@ebi.ac.uk> (Wolfgang Huber's message of "Mon, 26 Mar 2007 15:26:12 +0100")
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
way.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org