[BioC] GO enrichment for genome-wide analysis

[Peter.Robinson@t-online.de]

(... snip...)
> > 
> > http://david.niaid.nih.gov/david/ease.htm
> 
> Note that if you do use the above link, it will typically ask for a
> "background" set; this is meant to be a prompt to the user to think about
> what the actual background set should be.  I realize that I may have given
> the wrong impression that these online tools "do it wrong".  They simply
> allow the user to do it wrong if he/she desires.
> 
> Sean
> 


There are scenarios where it makes sense to use the whole genome (proteome) as a population (background) set. One example is if you are examining the GO annotations for all
proteins in the proteome that have a certain type of sequence pattern. User's need to think carefully about data and parameters for any bioinformatics analysis and regard
the analysis in some way as an experiment that needs good planning to get a good answer.

Peter