[BioC] "Size" in summary() of "hyperGTest()

[Seth Falcon]

* On 2009-02-19 at 00:54 +0000 Sergei Manakov wrote:
> Thanks for your reply. You are right, indeed I have used conditional =
> TRUE, and that is the reason why "Size" differs. Sorry about that, I
> should have guessed that myself. However, I find the description of
> the option "conditional" rather short in the Vignette. Could you
> please maybe just in a few sentences explain what it exactly it does?
> That would be very helpful.

The help page for GOstats::hyperGTest has some detail:

     When 'conditional(p) == TRUE', the 'hyperGTest' function uses the
     structure of the GO graph to estimate for each term whether or not
     there is evidence beyond that which is provided by the term's
     children to call the term in question statistically
     overrepresented.

     The algorithm conditions on all child terms that are themselves
     significant at the specified p-value cutoff.  Given a subgraph of
     one of the three GO ontologies, the terms with no child categories
     are tested first.  Next the nodes whose children have already been
     tested are tested.  If any of a given node's children tested
     significant, the appropriate conditioning is performed.

You might also find some of the discussion in this paper helpful:

> citation("GOstats")

To cite GOstats in publications use:

  S Falcon and R Gentleman. Using GOstats to test gene lists for GO
  term association. Bioinformatics, 23(2):257-8, 2007.

+ seth

-- 
Seth Falcon | http://userprimary.net/user/