[BioC] question about biomaRt problem

[Heidi Dvinge]

AFAIK, in Ensembl v64 RefSeq DNA IDs were replaced by RefSeq mRNA and
RefSeq ncRNA in the filters and attributes sections. However, there are
still a few stragglers lurking about as the RefSeg DNA.

Cheers
\Heidi

> Dear Heidi,
> thanks!
>
> Dear Steffen,
> it seems that the code example in the biomaRt vignette where Rong got
> this from would benefit from being updated.
>
> 	Best wishes
> 	Wolfgang
>
>
>
>
>
> Heidi Dvinge scripsit 03/07/2012 10:49 PM:
>> 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
>
>
> --
> Best wishes
> 	Wolfgang
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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