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