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Question: BiomaRt: getLDS keeps returning NULL
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5.9 years ago by
Guest User12k
Guest User12k wrote:
Dear list, I am trying to use the getLDS function from the biomaRt package to get mouse homolog for human genes but whatever example I take the function getLDS keeps returning NULL. > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53",mart = human,attributesL = c("chromosome_name","start_position"), martL = mouse) NULL Message d'avis : In getLDS(attributes = c("hgnc_symbol", "chromosome_name", "start_position"), : getLDS returns NULL. Thank you for your help Nolwenn -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.12.0 mouse4302.db_2.7.1 BiocInstaller_1.4.9 [4] org.Mm.eg.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] IRanges_1.14.4 RCurl_1.95-3 XML_3.95-0.1 stats4_2.15.0 tcltk_2.15.0 [6] tools_2.15.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.9 years ago by Nolwenn Le Meur10 • written 5.9 years ago by Guest User12k
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gravatar for Steffen Durinck
5.9 years ago by
Steffen Durinck530 wrote:
Hi Nolwenn, It looks like the linking of two datasets is currently broken at the Ensembl side. We've contacted them to look into it and hopefully this can be fixed soon. Cheers, Steffen On Wed, Nov 28, 2012 at 7:02 AM, Nolwenn Le Meur [guest] < guest@bioconductor.org> wrote: > > Dear list, > > I am trying to use the getLDS function from the biomaRt package to get > mouse homolog for human genes but whatever example I take the function > getLDS keeps returning NULL. > > > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > > getLDS(attributes = c("hgnc_symbol","chromosome_name", > "start_position"), filters = "hgnc_symbol", values = "TP53",mart = > human,attributesL = c("chromosome_name","start_position"), martL = mouse) > NULL > Message d'avis : > In getLDS(attributes = c("hgnc_symbol", "chromosome_name", > "start_position"), : > getLDS returns NULL. > > Thank you for your help > Nolwenn > > > -- output of sessionInfo(): > > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.12.0 mouse4302.db_2.7.1 BiocInstaller_1.4.9 > [4] org.Mm.eg.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 > [7] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 RCurl_1.95-3 XML_3.95-0.1 stats4_2.15.0 > tcltk_2.15.0 > [6] tools_2.15.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.9 years ago by Steffen Durinck530
Hi Nolwenn, Ensembl let us know that this is a known bug in the current Ensembl release 69 and that it will be fixed in the next release Ensembl 70 which is due sometime in january. Until that fix, I would suggest you query an archived version of Ensembl, the May release of this year works for example: library(biomaRt) human<-useMart("ENSEMBL_MART_ENSEMBL","hsapiens_gene_ensembl",host=" may2012.archive.ensembl.org") mouse<-useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl",host=" may2012.archive.ensembl.org") getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53",mart = human,attributesL = c("chromosome_name","start_position"), martL = mouse) HGNC.symbol Chromosome.Name Gene.Start..bp. Chromosome.Name.1 1 TP53 17 7565097 11 Gene.Start..bp..1 1 69393861 Cheers, Steffen On Wed, Nov 28, 2012 at 11:17 AM, Steffen Durinck <durinck.steffen@gene.com>wrote: > Hi Nolwenn, > > It looks like the linking of two datasets is currently broken at the > Ensembl side. > We've contacted them to look into it and hopefully this can be fixed soon. > > Cheers, > Steffen > > On Wed, Nov 28, 2012 at 7:02 AM, Nolwenn Le Meur [guest] < > guest@bioconductor.org> wrote: > >> >> Dear list, >> >> I am trying to use the getLDS function from the biomaRt package to get >> mouse homolog for human genes but whatever example I take the function >> getLDS keeps returning NULL. >> >> > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") >> > getLDS(attributes = c("hgnc_symbol","chromosome_name", >> "start_position"), filters = "hgnc_symbol", values = "TP53",mart = >> human,attributesL = c("chromosome_name","start_position"), martL = mouse) >> NULL >> Message d'avis : >> In getLDS(attributes = c("hgnc_symbol", "chromosome_name", >> "start_position"), : >> getLDS returns NULL. >> >> Thank you for your help >> Nolwenn >> >> >> -- output of sessionInfo(): >> >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.12.0 mouse4302.db_2.7.1 BiocInstaller_1.4.9 >> [4] org.Mm.eg.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 >> [7] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.14.4 RCurl_1.95-3 XML_3.95-0.1 stats4_2.15.0 >> tcltk_2.15.0 >> [6] tools_2.15.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.9 years ago by Steffen Durinck90
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gravatar for Nolwenn Le Meur
5.9 years ago by
Nolwenn Le Meur10 wrote:
Thank you Steffen for your help. I will do as you suggest. Best wishes Nolwenn On Friday, November 30, 2012, Steffen Durinck wrote: > Hi Nolwenn, > > Ensembl let us know that this is a known bug in the current Ensembl > release 69 and that it will be fixed in the next release Ensembl 70 which > is due sometime in january. > Until that fix, I would suggest you query an archived version of Ensembl, > the May release of this year works for example: > > library(biomaRt) > human<-useMart("ENSEMBL_MART_ENSEMBL","hsapiens_gene_ensembl",host=" > may2012.archive.ensembl.org") > mouse<-useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl",host=" > may2012.archive.ensembl.org") > getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), > filters = "hgnc_symbol", values = "TP53",mart = human,attributesL = > c("chromosome_name","start_position"), martL = mouse) > HGNC.symbol Chromosome.Name Gene.Start..bp. Chromosome.Name.1 > 1 TP53 17 7565097 11 > Gene.Start..bp..1 > 1 69393861 > > Cheers, > Steffen > > > > On Wed, Nov 28, 2012 at 11:17 AM, Steffen Durinck < > durinck.steffen@gene.com <javascript:_e({}, 'cvml',=""> 'durinck.steffen@gene.com');>> wrote: > >> Hi Nolwenn, >> >> It looks like the linking of two datasets is currently broken at the >> Ensembl side. >> We've contacted them to look into it and hopefully this can be fixed soon. >> >> Cheers, >> Steffen >> >> On Wed, Nov 28, 2012 at 7:02 AM, Nolwenn Le Meur [guest] < >> guest@bioconductor.org <javascript:_e({}, 'cvml',="">> 'guest@bioconductor.org');>> wrote: >> >>> >>> Dear list, >>> >>> I am trying to use the getLDS function from the biomaRt package to get >>> mouse homolog for human genes but whatever example I take the function >>> getLDS keeps returning NULL. >>> >>> > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >>> > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") >>> > getLDS(attributes = c("hgnc_symbol","chromosome_name", >>> "start_position"), filters = "hgnc_symbol", values = "TP53",mart = >>> human,attributesL = c("chromosome_name","start_position"), martL = mouse) >>> NULL >>> Message d'avis : >>> In getLDS(attributes = c("hgnc_symbol", "chromosome_name", >>> "start_position"), : >>> getLDS returns NULL. >>> >>> Thank you for your help >>> Nolwenn >>> >>> >>> -- output of sessionInfo(): >>> >>> R version 2.15.0 (2012-03-30) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_2.12.0 mouse4302.db_2.7.1 BiocInstaller_1.4.9 >>> [4] org.Mm.eg.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 >>> [7] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.14.4 RCurl_1.95-3 XML_3.95-0.1 stats4_2.15.0 >>> tcltk_2.15.0 >>> [6] tools_2.15.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org <javascript:_e({}, 'cvml',="">>> 'Bioconductor@r-project.org');> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.9 years ago by Nolwenn Le Meur10
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