[Bioc-devel] assayDat and ExpressionSet

[Martin Morgan]

Vincent Carey 525-2265 <stvjc at channing.harvard.edu> writes:

>> Of course.
>>
>> While I am at it: we are dropping phenoData completely right? It is a
>> bit confusing that all the new classes have phenoData slots which are
>> of class AnnotatedDataFrame. Well, it is mostly confusing because the
>> phenoData class is still around.
>
> i think the phenoData class should be defunct at next release,
> but the slots should retain their names.
>
>> Shouldn't varLabels(annotatedDataFrame) return object at varMetadata
>> $labelDescription if the varMetadata slot exists instead of as now

Valid objects always have the slot, with labelDescription always
present.

>> where it just yields names(object at data)

names(pData(object)) ;)

> that seems like a reasonable expectation.

varLabels suggests variable labels rather than label
descriptions. This was from the time before me, but I'd always thought
of the use in an interactive context and primarily at the
ExpressionSet level -- what are the labels of the covariates in this
analysis? Oh yes, now I'll ExpressionSet$whatever. Since varLabels is
a generic, and since a variety of different classes in and out of
Biobase use AnnotatedDataFrame, you'll be changing a lot of output.

Current use trumps a lot of change. There will be many people who
rightly expect varLabels to do what it has done for the last several
years. Better (in my opinion) alternatives are

- labelDescription generic + methods
- varMetadata(obj)$labelDescription

> there is a BiobaseDevelopment.Rnw of 4 Sept. 2006(!) in Biobase/inst/doc
> that seems to be the current locus classicus on eSet and descendants.
> this should be revisited and made definitive for 2.1 ... i will try to put
> some effort into this -- after i read it!
>
>
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