On Fri, Apr 11, 2008 at 11:41 AM, Gonzalo G?mez <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 G?mez L?pez
> Bioinformatics Unit
> Spanish National Cancer Research Center, CNIO.
> 3 Melchor Fern?ndez 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 escribi?:
>
>
>
> > On Fri, Apr 11, 2008 at 11:06 AM, Gonzalo G?mez <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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