[BioC] dead or alive vignette in biomaRt? was: question about biomaRt problem

[Wolfgang Huber]

Dear Steffen

thank you. I understand your argument: in some cases, the code in the 
vignette may fail due to transient network or server problems (I wonder 
how often this is nowadays still the case?). Unfortunately, it can also 
fail due to persistent changes in the content of the queried BioMart 
databases. I think an automated way of catching the latter is important 
- rather than putting this burden on users, who may be unexperienced and 
might get quite frustrated.

Does anyone have a clever idea on how to solve this dilemma?
	
	Best wishes
	Wolfgang


Mar/12/12 4:46 PM, Steffen Durinck scripsit::
> 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 at embl.de
> <mailto:whuber at 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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>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber