[BioC] question about biomaRt problem

[Heidi Dvinge]

Hi Rong>
> Hello,
> when I use the biomaRt package from R/bioconductor,
> there appears a problem:
> library("biomaRt")
> ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
> refseqinds=c("NM_005359","NM_000546")
> ipro=getBM(attributes=c("refseq_dna","interpro","interpro_description"),filters="refseq_dna",values=refseqinds,mart=ensembl)
>

it looks like you're using RefSeq *mRNA* IDs, not *DNA* IDs. The following
works:

> ipro=getBM(attributes=c("refseq_mrna","interpro","interpro_description"),filters="refseq_mrna",values=refseqinds,mart=ensembl)
> ipro
  refseq_mrna  interpro         interpro_description
1   NM_000546 IPR011615      p53, DNA-binding domain
2   NM_000546 IPR010991  p53, tetramerisation domain
3   NM_000546 IPR013872   p53 transactivation domain
4   NM_000546 IPR002117 p53 tumour suppressor family
5   NM_005359 IPR001132    SMAD domain, Dwarfin-type
6   NM_005359 IPR003619 MAD homology 1, Dwarfin-type
7   NM_005359 IPR013019            MAD homology, MH1

HTH
\Heidi


> ipro
> [1] refseq_dna interpro interpro_description <0 rows> (or 0-length
> row.names)
>
> Can anyone tell me what's the problem? Are there any other way to retrieve
> the gene name from refseq gene ID?
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.10.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.14.1 XML_3.9-4
>
>
> --
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>
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