[BioC] GOstats and GenePix arrays
rgentlem
rgentlem at fhcrc.org
Fri May 12 20:55:24 CEST 2006
Hi,
Mikko Arvas wrote:
>
> 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 am not sure what you might expect to find. AnnBuilder works on any
input data sources and the mechanism for combining different sources is
entirely under your control. We do not have a special page for organisms
with one data source and a different one for those with two etc, since
it is not needed. Which of the vignettes for AnnBuilder have you read?
If your organism is not well documented at one of the places that we
know about and use for AnnBuilder then you would need to use the tools
AnnBuilder provides to do that (and there has been quite some discussion
of this). AFAIK anyone who has taken building such a package seriously
has achieved their goal and we have provided assistance to some as
needed and will continue to do so.
> 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
The vignettes, and then Google on AnnBuilder led me to a lot of
documentation, both by us and by others who have used AnnBuilder,
and asking questions when you get stuck (please read the posting guide
as it will help you to get answers)
best wishes
Robert
>
> 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
>>
>> _______________________________________________
>> 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
>
>
> Mikko Arvas
>
> VTT
> Industrial Biotechnology
>
> e-mail: mikko.arvas at vtt.fi
> tel: +358-(0)20-722 5827
> mobile: +358-(0)44-381 0502
> fax: +358-(0)20-722 7071
> mail: Tietotie 2, Espoo
> P.O. Box 1000
> FI-02044 VTT, Finland
> VTT's website:
> http://www.vtt.fi/
> Protein production's website:
> http://www.vtt.fi/palvelut/cluster4/topic4_3/Proteiinin_tuotto.jsp?lang=en
>
> Welcome to Yeast Systems Biology meeting ISSY25, http://issy25.vtt.fi/
> organised by VTT.
>
>
--
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
More information about the Bioconductor
mailing list