[BioC] Fwd: Re: Run GOHyperG without specifying a chip

[Mikko Arvas]

>Date: Fri, 17 Feb 2006 10:48:56 +0200
>To: bioconductor.stat.math.ethz.ch
>From: Mikko Arvas <Mikko.Arvas at vtt.fi>
>Subject: Re: [BioC] Run GOHyperG without specifying a chip
>
>At 12:08 16.2.2006 -0800, you wrote:
>>Hi,
>>    Jim is right, but we should split out the different parts, all that
>>the chip is used for is to define the universe and it is perfectly
>>reasonable to want to define your own universe. Look for some changes in
>>the devel arm later this week. One problem with that approach is that we
>>will have no way to test that your Entrez Gene IDs are valid, so that is
>>going to require that the user take all responsibility on that front
>>(and it could have a big effect if you accidently add in a bunch of
>>non-Entrez gene ids).
>>
>>    best wishes
>>     Robert

Hi,

remotely related to this I am working on a recently sequenced fungi and
not having a clue how to build an actual annotation package (I couldn't figure
out it from the vignettes, but maybe there is better documentation somewhere,
but anyhow I don't know R very well),  I just constructed a genomic GO list 
like this
based on INTERPRO hits for my own fun  (where treXXXX is a gene id):
$tre41841
$tre41841$"GO:0006508"
$tre41841$"GO:0006508"$GOID
[1] "GO:0006508"
$tre41841$"GO:0006508"$Evidence
[1] "IEA"
$tre41841$"GO:0006508"$Ontology
[1] "BP"
$tre41841$"GO:0004194"
$tre41841$"GO:0004194"$GOID
[1] "GO:0004194"
$tre41841$"GO:0004194"$Evidence
[1] "IEA"
  etc ...

could one pass something like this to GOhyperG as the universe
or do I have to make something like the YEAST package for my fungi?
How does one make GOHyperG work with YEAST package?

Cheers,
Mikko


Mikko Arvas

VTT
Industrial Biotechnology

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