>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 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?lan g=en Welcome to Yeast Systems Biology meeting ISSY25, http://issy25.vtt.fi/ organised by VTT.