[BioC] Agilent IDs and biomaRt package

[Sean Davis]

On Fri, Apr 11, 2008 at 11:41 AM, Gonzalo Gómez <ggomez at cnio.es> wrote:
> Hi Sean, the commas are introduced in the original code, I lost them in the
> e-mail :-) So the AgiIDs object is ok in the original code. My sessionInfo:

And how about the quotation marks?  This works fine for me:

> library(biomaRt)
Loading required package: RCurl
> ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
Checking attributes and filters ... ok
> AgiIDs<-c("A_51_P227502" "A_52_P330395" "A_51_P183051")
Error: unexpected string constant in "AgiIDs<-c("A_51_P227502" "A_52_P330395""
> AgiIDs<- c("A_51_P227502" "A_52_P330395" "A_51_P183051")
Error: unexpected string constant in "AgiIDs<- c("A_51_P227502" "A_52_P330395""
> AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051")
> Agilent<-getGene(AgiIDs, type = 'agilent_probe', mart=ensembl)
> Agilent
  agilent_probe mgi_symbol
1  A_51_P183051       Upb1
2  A_51_P227502      Mfap2
3  A_52_P330395      Farp1


description
1         Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase)
(N- carbamoyl-beta-alanine amidohydrolase).
[Source:Uniprot/SWISSPROT;Acc:Q8VC97]
2 Microfibrillar-associated protein 2 precursor (MFAP-2) (Microfibril-
associated glycoprotein) (MAGP) (MAGP-1).
[Source:Uniprot/SWISSPROT;Acc:P55002]
3
FERMRhoGEF (Arhgef) and pleckstrin domain protein 1
[Source:RefSeq_peptide;Acc:NP_598843]
  chromosome_name band strand start_position end_position    ensembl_gene_id
1              10 B5.3      1       74869760     74904424 ENSMUSG00000033427
2               4   D3      1      140566596    140571882 ENSMUSG00000060572
3              14   E4      1      121434766    121682948 ENSMUSG00000025555


>  R version 2.4.1 (2006-12-18)
>  i386-apple-darwin8.8.1
>
>  locale:
>  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
>  attached base packages:
>  [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> "methods"   "base"
>  other attached packages:
>   biomaRt     RCurl       XML  mgu74av2 mgug4122a  annotate   Biobase
>   "1.8.2"   "0.8-0"   "1.7-2"  "1.14.0"  "1.14.0"  "1.12.1"  "1.12.2"
>
>  Thanks for your help...
>
>  Gonzalo
>
>
>
>
>
>
>  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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