[BioC] GOstats and GenePix arrays

[Jake]

I hadn't thought of going through the trouble of making a custom
annotation package.  Last time I tried making one was quite a while back
and it was quite a pain.  I'm sure things work more smoothly now, but by
looking at GOHyperG I realized all I really need is phyper and the
appropriate GO mappings, which I've gotten through TAIR and the use of
GOANCESTOR.

I guess in the light of making a custom annotation package, GOHyperG
isn't *technically* Affy-only, though with components like "go2Affy",
it's obvious what type of data was in mind.

Thanks for the comments and insight.

--Jake


On Thu, 2006-05-11 at 10:57 -0700, rgentlem wrote:
> 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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>