[BioC] counts vs exprs

[Wolfgang Huber]

Dear Ed

the documentation of eSet (try typing "class ? eSet" into R after 
loading Biobase) does not mention an exprs method. Perhaps you are 
confusing it with ExpressionSet.

A schematic interpretation is:
- ExpressionSet is for processed datasets and presents a uniform 
interface for downstream analyses (e.g. machine learning)
- Other eSet derived classes (e.g. countDataSet, NChannelSet, the 
cellHTS class in cellHTS2) are for 'matrix-like' raw data, and reflect 
their ideosyncrasis, which is useful and needed for technology-specific 
preprocessing algorithms. E.g. the data in a CountDataSet are 
non-negative integers.

Hope this helps
	Wolfgang

Apr/3/12 5:28 PM, Ed Siefker scripsit::
> I was trying out the DESeq package, whose documentation says:
>
> "The CountDataSet class is derived from Biobase’s eSet class and so
> shares all features of
> this standard Bioconductor class."
>
> So I tried exprs() on it, which didn't work.  Of course, CountDataSets
> have their own
> counts() function.  I was just wondering why they have different
> names.   Why not make
> count data accessible through exprs()?  Is the reasoning behind this
> due to R internals,
> or is it biologically motivated?
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber