[Bioc-devel] assayDat and ExpressionSet

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Tue Oct 16 04:06:15 CEST 2007

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

that seems like a reasonable expectation.

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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