Hi Wolfgang, Heidi,

I'll give the biomaRt vignette an update later this week.  All examples in
the vignette used to be run during the package building process but often
the build would fail due to internet connection problems or slow server
responses, issues unrelated to the biomaRt package itself.  This is the
main reason why I deactivated running them as there was often nothing wrong
with the examples but the package build would fail and I wanted to keep
many examples in the vignette so users can understand the wide variety of
different queries available to them through biomaRt.

Cheers,
Steffeb

On Thu, Mar 8, 2012 at 7:06 AM, Wolfgang Huber <whuber@embl.de> wrote:

> 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<http://www.embl.de/research/units/genome_biology/huber>
>
>
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