[BioC] GOstats and GenePix arrays

[Mikko Arvas]

Hi,

there must be a growing number of people working with own custom chips and
custom annotations for "exotic" half finished genomes, like me.
Atleast last time I checked I didn't really find anything addressing this 
situtation
in Annbuilder documentation or list archives.

I would be very happy for any advice on how to build an annotation package
from self made chipID-GOid (or any other annotation) lists. Maybe it's my lack
of experience, but I really don't know where to start

Cheers,
Mikko

At 11:17 11.5.2006 -0700, rgentlem wrote:


>Jake wrote:
> > 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.
> >
>
>   Well, if you don't go to the trouble, then you will almost surely be
>getting the wrong answer, and to paraphrase one of the really clever
>folks, there are easier and faster ways to do that :-)
>
> > 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
> >>>
> >>> _______________________________________________
> >>> 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
>
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Mikko Arvas

VTT
Industrial Biotechnology

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