[Bioc-devel] Bioc-devel Digest, Vol 36, Issue 13
sdavis2 at mail.nih.gov
Sun Mar 18 18:39:03 CET 2007
Simon Lin wrote:
> Dear Adi,
> I see your points but I disagree.
> A gene list is always derived from somewhere. Thus, there are particular
> experiments associated with it. Under this particular experimental setting,
> there are stereotypes of UP and DOWN. With that being said, we can also find
> metadata associated with a gene list is important to keep.
> As such, I think the directions make sense; although mathematically the sign
> can be flipped, biologists have predefined contexts of UP and DOWN.
In my mind, there will be a "generic" geneSet class. Then, there can be
subclasses for directionalGeneSet (up/down) and rankedGeneSet (with
quantitative ranking information). I don't think these extra metadata
need to be in the main geneSet class.
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