[Bioc-devel] Bioc-devel Digest, Vol 36, Issue 13

Sean Davis 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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