[BioC] Agilent IDs and biomaRt package

[Sean Davis]

On Fri, Apr 11, 2008 at 11:48 AM, Gonzalo Gómez <ggomez at cnio.es> wrote:
> Dear Sean,
>
>  extra quotes around agilent_probe and agilent works :-)
>
>
>  getBM(attributes = c("chromosome_name", "start_position"),
> filters="agilent_probe", values = AgiIDs, mart = ensembl)
>  thanks
>

Great.

>
>
>  G
>
>  Have you tried CARGO???
>  http://cargo.bioinfo.cnio.es/
>
>  *****************************
>
>  Gonzalo Gómez López
>  Bioinformatics Unit
>  Spanish National Cancer Research Center, CNIO.
>  3 Melchor Fernández Almagro st.
>  Madrid 28029
>  Spain
>  ggomez at cnio.es
>  http://www.cnio.es
>
>  Lab Phone: +34 91 732 80 00 (ext 3062)
>  Fax: +34 91 224 69 76
>  Skype: gonzalo.gomez7
>
>  *****************************
>
>
>
>  Sean Davis escribió:
>
> > On Fri, Apr 11, 2008 at 11:06 AM, Gonzalo Gómez <ggomez at cnio.es> wrote:
> >
> >
> > > Hi all! I am trying to make a simple query for Agilent IDs in ensembl
> > >  using biomaRt package. The code seems to be simple and vignettes are
> > >  clear, however it fails...Im not sure if this could be a bug in biomaRt
> > >  or in my code
> > >
> > >  #My code is :
> > >
> > >  >library(biomaRt)
> > >  >ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
> > >  >AgiIDs<-c("A_51_P227502" "A_52_P330395" "A_51_P183051")
> > >
> > >  #I´ve tried:
> > >
> > >  >Agilent<-getGene(AgiIDs, type = agilentprobe, mart=ensembl)
> > >  Error in inherits(x, "factor") : object "agilentprobe" not found
> > >
> > >  #and:
> > >
> > >  >getBM(attributes = c("chromosome_name", "start_position"),
> > >  filters=agilent-probe-2, values = AgiIDs, mart = ensembl)
> > >  Error in inherits(x, "factor") : object "agilent" not found
> > >
> > >  I´ve used listFilters(ensembl) in order to find the correct filters and
> > >  type parametres and I also have used: agilent_probe but it doesn´t work
> > >  anymore...
> > >
> > >  >Agilent<-getGene(AgiIDs, type = agilent_probe, mart=ensembl)
> > >  Error in inherits(x, "factor") : object "agilent_probe" not found
> > >  >getBM(attributes = c("chromosome_name", "start_position"),
> > >  filters=agilent_probe, values = AgiIDs, mart = ensembl)
> > >  Error in inherits(x, "factor") : object "agilent_probe" not found
> > >
> > >
> > >  Please, I´ll be very thankful if anybody can help me with this...
> > >
> > >
> >
> > Hi, Gonzalo.  Your AgiIDs needs some commas.  I think you need some
> > extra quotes around agilent_probe and agilent?  Does that help?  If
> > not, do not forget to include sessionInfo() if you need more help.
> >
> > Sean
> >
> >
>
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