[BioC] GOstats and GenePix arrays

[rgentlem]

Hi,

  I am not sure why you think that you should do anything different for 
GenePix? The array used is completely irrelevant to this sort of 
hypergeometric testing and there should be no need to modify GOstats in 
any way.
  You simply make an annotation package for your array (using AnnBuilder 
or any other tool of your choice) and then use it.

  best wishes
   Robert

Jake wrote:
> Hi all,
> 
> I'm trying to use the "guts" of the GOHyperG function in GOstats as a
> basis for a similar function for GenePix data.  I've found a basic
> description of the phyper function in the context of GO:
> 
> # How to implement phyper function for GO analysis
> #       phyper(x-1, m, n-m , k, lower.tail = FALSE)
> #       x: number of sample genes at GO node (can be vector with many
> entries)
> #       m: number of genes at GO node (works with vector of same length
> as x)
> #       n: number of unique genes at all GO nodes
> #       k: number of unique genes in test sample that have GO mappings
> 
> Values for x and k seem straightforward, but I'm wondering about m and
> n.  The arrays we're working with seem to have fewer genes on them than
> the total number cataloged in the organism's online databases.  So
> should m and n be based on the absolute total number of genes annotated,
> or the number of genes annotated *on the chip*?
> 
> Thanks in advance,
> 
> Jake
> 
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-- 
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