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

[Robert Gentleman]

Hi Sergei,
   Sorry to be so slow in getting back to you.

On Tue, Feb 17, 2009 at 3:40 AM, Sergei Manakov <manakov at ebi.ac.uk> wrote:
> Hello,
>
> I assume that "Size" column in the table generated by summary() of
> "GOHyperGResult" object produced by hyperGTest() function from
> "GOstats" package is the total size of a given GO category.

 Not necessarily, it will depend on a number of factors (some of them
depend on parameters you have set).
  So, first, it does depend on the gene universe, but it also will
vary if you have set conditional=TRUE, as in that case any significant
children are excluded - which is what conditional means, in this
setting.  I believe you will find that they are always identical if
you set conditional=FALSE, but please let me know if not, and in that
case, if you could follow the posting guide and provide details such
as sessionInfo() and a small example, I can try to be more helpful.

  best wishes
   Robert
>
> In this regard I am puzzled why values in this field are slightly
> different for the same GO categories when I run the  hyperGTest() on
> different query gene lists, even when using the same Universe.
>
> I would be grateful for any suggestions.
>
> thanks,
> Sergei
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>



-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org