[BioC] dead or alive vignette in biomaRt? was: question about biomaRt problem
Wolfgang Huber
whuber at embl.de
Tue Mar 13 22:40:30 CET 2012
Dear Kasper
yes. Probably better even would be to wrap the initial 'actual' attempt
to connect to the server in a tryCatch. If successful, execute the rest
of the vignette, if not, replace it with a cached one, and eventually,
if that happens repeatedly, send someone (e.g. the maintainer) a warning.
It is a pity that the Sweave syntax does not make it easier to do
computations on the document.
Best wishes
Wolfgang
Mar/13/12 10:29 PM, Kasper Daniel Hansen scripsit::
> 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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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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