[Bioc-devel] assayDat and ExpressionSet

Wolfgang Huber huber at ebi.ac.uk
Thu Oct 18 21:21:31 CEST 2007


Vincent Carey 525-2265 wrote:
> i think the phenoData class should be defunct at next release,
> but the slots should retain their names.

I think "featureData" and "sampleData" would be more consistent as the 
prefered accessor functions to the annotatedDataframes for annotating 
'rows' and 'colums' of an eSet, respectively.

I don't care too much how the slot in the class implementation is 
called, but if our software is what we claim it is, we might as well 
also be able to rename the eSet slot "phenoData" to "sampleData", and 
keep accessor functions named phenoData and phenoData<- (that do the 
same as sampleData...) still around for a couple of releases.

This is a long-term question of low urgency, but I do find it important 
for the user experience that we call things by their proper names and 
not use inexact and potentially confusing terminology (or doesn't it 
make you whince when your biological collaborators talk of "p-values" 
when they mean regression coefficients?)

  Best wishes

>> 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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