Hi Steffen, Thanks for you quick reply, I will try it again next week then. In reply to you request; I just c/p your lines in above post and it resulted in said error message. I don't know if it helps but I did find a remark related to something similar: I believe biomaRt package does not support the new webservice API of biomart v0.8. It should work if your biomart installation was v0.7. source: http://comments.gmane.org/gmane.science.biology.informatics.conductor/ 40152 I use ubuntu 12.04.1, R2.15 best wishes Steven 2013/1/28 Steffen Durinck <durinck.steffen@gene.com> > Hi Steven, > > The ensembl web interface has been updated to Ensembl 70 but the BioMart > interface not yet, this usually happens about a week or so later. If you > use listMarts() you can see that biomaRt is still giving ENSEMBL GENES 69 > (SANGER UK) as version and not 70. I would expect the BioMart interface to > be updated soon too and hopefully your query then works. > > Can you give the exact query you were attempting to the archive that gave > you the XML error So I can look into why it fails? > > Cheers, > Steffen > > > On Mon, Jan 28, 2013 at 9:23 AM, Steven <steven.wink@gmail.com> wrote: > >> Dear list, >> >> In relation to above posts, I am also not getting getLDS to work. Steffen >> mentioned the ensemble 70 release could possibly fix the linking of db's, >> but it is not working for me yet. >> using the lines from Nolwenn I also get zero rows output. Using Steffens >> solution of an archived ensemble version I get an api error: >> >> Request to BioMart web service failed. Verify if you are still connected >> to the internet. Alternatively the BioMart web service is temporarily >> down. Check http://www.biomart.org and verify if this website is >> available. >> *Error: XML content does not seem to be XML, nor to identify a file name >> * >> >> I would like to map e.g. affy probe ID's from "affy_hg_u133_plus"_2 to >> "affy_rat230_2". >> >> An alternative solution to using biomaRt would also be super. >> >> best Wishes, >> >> Steven Wink >> >> >> >> 2012/11/30 Nolwenn Le Meur <nlemeur@gmail.com> >> >>> 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]] >>> >>> >>> _______________________________________________ >>> 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]]