2010/11/12 Clémentine Dressaire <clementinedressaire@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@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
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >
>
> > _______________________________________________
>
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>
> > Bioconductor@stat.math.ethz.ch
>
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>
> > 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
>
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