Hi Steffen,

I thought of getting Ensemble IDs for my genes before I extract SNPs. So, I
have used:

ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")

getBM(attributes = c("hgnc_symbol","ensembl_gene_id","entrezgene",
"chromosome_name", "start_position", "end_position"), filters="hgnc_symbol",
values=gene, mart = ensembl)

Is this because I am using an old version of R (2.9.0)?

Thanks,
Sharon


sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.95-1 XML_2.3-0

On Tue, Oct 20, 2009 at 10:51 PM, <Steffen@stat.berkeley.edu> wrote:

> Hi Sharon,
>
> Can you give the exact query you were performing?  This is not a desired
> error and has to do with a feature of the SNP BioMart that needs to be
> resolved.  The error might go away by removing a specific attribute from
> your query.
>
> Cheers,
> Steffen
>
>
> > Dear Vincent,
> >
> > Though I get required info, I do get the following error message:
> >
> > Error in getBM(mart = .gmart, filters = "hgnc_symbol", value = gname,  :
> >   The query to the BioMart webservice returned an invalid result: the
> > number
> > of columns in the result table does not equal the number of attributes in
> > the query. Please report this to the mailing list.
> >
> > Do I need to consider this seriously?
> >
> > Thanks again,
> > Sharon
> >
> > On Tue, Oct 20, 2009 at 12:12 PM, Vincent Carey
> > <stvjc@channing.harvard.edu>wrote:
> >
> >> if you add a function like this to your workspace, you can query on rs
> >> number for some of the items you mention.  other retrieval approaches
> >> could be based on NCBI eutils.
> >>
> >> qsnp <- function (rsid, attrs = c("chr_name", "chrom_start", "allele",
> >>    "associated_variant_risk_allele", "risk_allele_freq_in_controls",
> >>    "allele_1", "associated_gene", "phenotype_description", "validated",
> >>    "ensembl_peptide_shift"))
> >> {
> >>    if (!exists(".HSmart"))
> >>        .HSmart <<- useMart(biomart = "snp", dataset = "hsapiens_snp")
> >>    getBM(mart = .HSmart, filters = "refsnp", value = rsid, attributes =
> >> attrs)
> >> }
> >>
> >> > qsnp("rs13087941")
> >>  chr_name chrom_start allele associated_variant_risk_allele
> >> 1        3     8787220    T/C                             NA
> >> 2        3     8787220    T/C                             NA
> >>  risk_allele_freq_in_controls allele_1 associated_gene
> >> phenotype_description
> >> 1                           NA        C              NA
> >>  NA
> >> 2                           NA        C              NA
> >>  NA
> >>                      validated ensembl_peptide_shift
> >> 1 cluster,freq,doublehit,hapmap                    NA
> >> 2 cluster,freq,doublehit,hapmap                 FALSE
> >>
> >> be prepared for certain ambiguities to crop up
> >>
> >> > qsnp("rs10000")
> >>  chr_name chrom_start allele associated_variant_risk_allele
> >> 1        7     6013153    T/C                             NA
> >> 2        7     6013153    T/C                             NA
> >> 3        7     6790900    T/C                             NA
> >>  risk_allele_freq_in_controls allele_1 associated_gene
> >> phenotype_description
> >> 1                           NA       NA              NA
> >>  NA
> >> 2                           NA       NA              NA
> >>  NA
> >> 3                           NA       NA              NA
> >>  NA
> >>     validated ensembl_peptide_shift
> >> 1 cluster,freq
> >> 2 cluster,freq                     L
> >> 3 cluster,freq
> >>
> >>
> >> On Tue, Oct 20, 2009 at 5:11 AM, Sharon <sharonanandhi@gmail.com>
> wrote:
> >> > Dear All,
> >> >
> >> > Thanks a lot for your suggestions. I did try with biomaRt to get CHR
> >> and
> >> POS
> >> > info for SNPs. When I query dbSNP for a particular gene (Geneview
> >> report),
> >> > we do get useful information such as validation, function and protein
> >> > residue etc. for SNPs. Is it possible to get these information using
> >> > biomaRt? If so, could you please tell me where can I find info for
> >> > appropriate fields?
> >> >
> >> > Thanks again.
> >> >
> >> > Kind regards,
> >> > Sharon
> >> >
> >> >
> >> > On Mon, Oct 19, 2009 at 10:38 PM, <Steffen@stat.berkeley.edu> wrote:
> >> >>
> >> >> Also to note is that biomaRt indeed queries Ensembl for SNP queries
> >> and
> >> >> these SNPs are from dbSNP mapped to Ensembl.
> >> >>
> >> >> The latest release notes from Ensembl 56 state:
> >> >>
> >> >> Ensembl variation mart 56
> >> >>
> >> >>    * Removal of Ensembl Celera, TSC and HGVBase information
> >> >>    * Human now on dbSNP 130
> >> >>
> >> >>
> >> >> Cheers,
> >> >> Steffen
> >> >>
> >> >> > It may also be noteworthy that the SNPlocs.Hsapiens.dbSNP.20090506
> >> >> > package has location and allele information for build 130 dbSNP
> >> >> > entries. A substantial quantity of SNP-related metadata is present
> >> in
> >> >> > the pd.genomewidesnp.6 annotation package.
> >> >> >
> >> >> >  'Queries' to dbSNP of a more general nature could probably be
> >> >> > programmed using various web services support packages in R/bioc.
> >> If
> >> >> > you describe a compelling use case, code might be written to solve
> >> it.
> >> >> >
> >> >> > On Mon, Oct 19, 2009 at 4:30 PM, Marc Carlson <mcarlson@fhcrc.org>
> >> >> > wrote:
> >> >> >> Hi Sharon,
> >> >> >>
> >> >> >> It's not clear to me from your email what you intend to do, but I
> >> know
> >> >> >> that some dbSNP data is available as a UCSC track and should
> >> therefore
> >> >> >> be obtainable by using the rtracklayer package.
> >> >> >>
> >> >> >>  Marc
> >> >> >>
> >> >> >>
> >> >> >> Sharon wrote:
> >> >> >>> Dear All,
> >> >> >>>
> >> >> >>> Is there any tool in Bioconductor to query dbSNP? I know that
> >> (correct
> >> >> >>> me,
> >> >> >>> if I am wrong) biomaRt is primarily for Ensemble.
> >> >> >>>
> >> >> >>> Thanks in advance.
> >> >> >>>
> >> >> >>> Kind regards,
> >> >> >>> Sharon.
> >> >> >>>
> >> >> >>>       [[alternative HTML version deleted]]
> >> >> >>>
> >> >> >>> _______________________________________________
> >> >> >>> Bioconductor mailing list
> >> >> >>> Bioconductor@stat.math.ethz.ch
> >> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> >>> Search the archives:
> >> >> >>>
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >> >>>
> >> >> >>>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> Bioconductor mailing list
> >> >> >> Bioconductor@stat.math.ethz.ch
> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> >> Search the archives:
> >> >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >> >>
> >> >> >
> >> >> > _______________________________________________
> >> >> > Bioconductor mailing list
> >> >> > Bioconductor@stat.math.ethz.ch
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> > Search the archives:
> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >> >
> >> >>
> >> >> _______________________________________________
> >> >> Bioconductor mailing list
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> >> >> Search the archives:
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> >> >
> >> >
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
>

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