[BioC] help with makeGOGraph
Clémentine Dressaire
clementinedressaire at itqb.unl.pt
Fri Nov 12 19:27:07 CET 2010
OK this was a glaring mistake from mine. I sincerely apologyze for
disturbing with such a stupid thing. I promise I'll pay more attention now
and think better before asking anything.
Sorry,
Clémentine
On Fri, 12 Nov 2010 13:16:01 -0500, Sean Davis <sdavis2 at mail.nih.gov>
wrote:
> 2010/11/12 Clémentine Dressaire <clementinedressaire at itqb.unl.pt>
>
>>
>> Hello again,
>>
>>
>>
>> I have completely forgotten to copy my session informations...
>>
>>
>>
>> > sessionInfo()
>>
>> R version 2.12.0 (2010-10-15)
>>
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>>
>>
>> locale:
>>
>> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
>>
>> LC_MONETARY=French_France.1252
>>
>> [4] LC_NUMERIC=C LC_TIME=French_France.1252
>>
>>
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods base
>>
>>
>>
>> other attached packages:
>>
>> [1] ecoli2cdf_2.6.0 gage_2.0.0 multtest_2.6.0
>>
>> ecoli2.db_2.4.7 org.EcK12.eg.db_2.4.6
>>
>> [6] simpleaffy_2.26.0 gcrma_2.22.0 genefilter_1.32.0
>>
>> annotate_1.28.0 biomaRt_2.6.0
>>
>> [11] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5
>>
>> lattice_0.19-13 affy_1.28.0
>>
>> [16] limma_3.6.0 GOstats_2.16.0 RSQLite_0.9-2
>>
>> DBI_0.2-5 graph_1.28.0
>>
>> [21] Category_2.16.0 AnnotationDbi_1.12.0 Biobase_2.10.0
>>
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] affyio_1.18.0 Biostrings_2.18.0 grid_2.12.0
>>
>> GSEABase_1.12.0 IRanges_1.8.0
>>
>> [6] MASS_7.3-8 preprocessCore_1.12.0 RBGL_1.25.1
>>
>> RCurl_1.4-4.1 splines_2.12.0
>>
>> [11] survival_2.35-8 tools_2.12.0 XML_3.2-0.1
>>
>> xtable_1.5-6
>>
>>
>>
>>
>>
>> As for an example if I use the following vector of EntrezGeneIds I get
a
>>
>> similar error message:
>>
>>
>>
>>
>>
>ex=c(947043,948258,2847747,2847746,946713,948679,948192,944872,946844,946841)
>>
>> > ex
>>
>> [1] 947043 948258 2847747 2847746 946713 948679 948192 944872
>>
>> 946844 946841
>>
>> >
makeGOGraph(ex,ontology="BP",removeRoot=T,mapfun=NULL,chip=ecoli2.db)
>>
>>
>>
>> Erreur dans makeGOGraph(ex, ontology = "BP", removeRoot = T, mapfun =
>>
>> NULL, :
>>
>> argument(s) inutilisé(s) (ontology = "BP")
>>
>>
> Try using "Ontology" instead of "ontology" for the argument. Note that
the
> capital letter is needed.
>
> Sean
>
>
>
>>
>>
>>
>>
>> Clémentine
>>
>>
>>
>>
>>
>>
>>
>> On Fri, 12 Nov 2010 09:12:18 -0800, Marc Carlson <mcarlson at fhcrc.org>
>>
>> wrote:
>>
>> > Hi Clémentine,
>>
>> >
>>
>> > Could you please give us your sessionInfo() and a reproducible
example?
>>
>> > That would allow us to be able to really find out what is happening
>>
>> > here. You might want find it helpful to have a peek at the posting
>>
>> > guide here:
>>
>> >
>>
>> > http://www.bioconductor.org/help/mailing-list/posting-guide/
>>
>> >
>>
>> >
>>
>> > Marc
>>
>> >
>>
>> >
>>
>> >
>>
>> >
>>
>> > On 11/12/2010 07:51 AM, Clémentine Dressaire wrote:
>>
>> >> Dear BioC users,
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> I am trying to construct a GOgraph using a gene list (overgenes[,3])
>> >> of
>>
>> >>
>>
>> >> messengers that I previously identified as overexpressed in the
>>
>> >> condition I
>>
>> >>
>>
>> >> was interested in. I previoulsy used this same gene list to perform
>>
>> >>
>>
>> >> hypergeometric tests and it worked well.
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> With makeGOgraph I systematically get the following error message,
>>
>> >>
>>
>> >> whichever ontology type I try to use:
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>>
>>
makeGOGraph(overgenes[,3],ontology="BP",removeRoot=F,mapfun=NULL,chip=ecoli2.db)
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Erreur dans makeGOGraph(overgenes[, 3], ontology = "BP",
>>
>> removeRoot
>>
>> >> =
>>
>> >>
>>
>> >> F, :
>>
>> >>
>>
>> >> argument(s) inutilisé(s) (ontology = "BP")
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> I wonder wether this could be due to the fact that some of the genes
>> >> in
>>
>> >>
>>
>> >> the list do not have GO annotation...(then does it mean that I have
to
>>
>> >>
>>
>> >> eliminate them? If so what would be the simplest way?)
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Does anyone can throw light on this issue for me?
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Many thanks for your help,
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Clémentine
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >
>>
>> > _______________________________________________
>>
>> > 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
>>
>>
>>
>> --
>>
>> Clémentine Dressaire
>>
>> Post-doctoral research fellow
>>
>> Control of gene expression lab
>>
>> ITQB - Instituto de Tecnologia Química e Biológica
>>
>> Apartado 127, Av. da República
>>
>> 2780-157 Oeiras
>>
>> Portugal
>>
>> +351 214469562
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
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--
Clémentine Dressaire
Post-doctoral research fellow
Control of gene expression lab
ITQB - Instituto de Tecnologia Química e Biológica
Apartado 127, Av. da República
2780-157 Oeiras
Portugal
+351 214469562
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