question about biomaRt problem
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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) 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 -- Sent via the guest posting facility at bioconductor.org.
biomaRt biomaRt • 2.1k views
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Heidi Dvinge ★ 2.0k
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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_descriptio n"),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_descripti on"),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 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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_descripti on"),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_descript ion"),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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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_descript ion"),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_descrip tion"),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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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=""> > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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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","__int erpro_description"),__filters="refseq_dna",values=__refseqinds,mart=en sembl) > > > it looks like you're using RefSeq *mRNA* IDs, not *DNA* IDs. The > following > works: > > ipro=getBM(attributes=c("__refseq_mrna","interpro","__in terpro_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=""> > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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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_desc ription"),__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_des cription"),__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=""> >> >> >> ? ?_________________________________________________ >> ? ?Bioconductor mailing list >> ? ?Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> ? ?https://stat.ethz.ch/mailman/__listinfo/bioconductor >> ? ?<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> ? ?Search the archives: >> ? ?http://news.gmane.org/gmane.__science.biology.informatics.__conductor >> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> >> > > > -- > Best wishes > ? ? ? ?Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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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_de scription"),__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_d escription"),__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=""> >>> >>> >>> _________________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> >> >> >> -- >> Best wishes >> Wolfgang >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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