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

[Kasper Daniel Hansen]

Writing a command that pings the biomaRt server on is trying to
connect to and returns TRUE if the pinging works (assuming that the
server accepts pings) is probably a very good way to start.

Kasper

On Tue, Mar 13, 2012 at 5:19 PM, Wolfgang Huber <whuber at embl.de> wrote:
> 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
>
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