Hi Katleen, I am cc'ing Steffen Durinck who is an expert on the R interface and hopefully will be able to help you with that
a On Tue, Nov 27, 2012 at 12:32 PM, Katleen De Preter < [email protected]> wrote: > Dear Arek,**** > > > Thanks for your reply. However, it is still not working (via R): did > something change in the structure of the database, so that the following R > script doesn’t work anymore?**** > > ** ** > > library(biomaRt)**** > > human<-useMart("ensembl","hsapiens_gene_ensembl") #define human > database, it works**** > > zebrafish<-useMart("ensembl","drerio_gene_ensembl") #define > zebrafishdatabase, it works > **** > > homolog.1<-getLDS(attributes=c("external_gene_id"),filters =" > wikigene_name",values =my.list1,mart=human,**** > > attributesL=c("hgnc_symbol"),martL=zebrafish) # this > last code line gives no results**** > > ** ** > > Or can you help me how to configure the online biomart request in order > to get human gene symbols vs zebrafish gene symbols (and not only ensembl > IDs).**** > > ** ** > > Kind regards,**** > > ** ** > > Katleen De Preter**** > > ** ** > > *From:* Arek Kasprzyk [mailto:[email protected]] > *Sent:* dinsdag 27 november 2012 11:52 > *To:* Katleen De Preter > *Cc:* [email protected] > *Subject:* Re: [BioMart Users] General query: ortholog searches**** > > ** ** > > Hi Katleen,**** > > We have recently updated the server to Ensembl 69, perhaps this was just a > temporary glitch**** > > ** ** > > The following query : > http://www.biomart.org/biomart/martview/1456454c60d2a4397ffb57525b5acbb3** > ** > > ** ** > > produces the output:**** > > ** ** > > Ensembl Gene ID Ensembl Transcript ID Zebra Finch Ensembl > Gene ID Mouse Ensembl Gene ID**** > > ENSG00000259662 ENST00000539570 ENSTGUG00000003187 > ENSMUSG00000050503**** > > ENSG00000258865 ENST00000510508 ENSTGUG00000012784 > ENSMUSG00000075707**** > > ENSG00000258664 ENST00000553856 ENSMUSG00000079252**** > > ENSG00000258518 ENST00000483851 ENSTGUG00000011221 > ENSMUSG00000027833**** > > ENSG00000259741 ENST00000558098 ENSTGUG00000000764 > ENSMUSG00000021156**** > > ENSG00000259741 ENST00000558098 ENSTGUG00000017137 > ENSMUSG00000021156**** > > ENSG00000265969 ENST00000292095 ENSTGUG00000000184 > ENSMUSG00000032086**** > > ENSG00000262355 ENST00000305831 ENSTGUG00000014163 > ENSMUSG00000021838**** > > ENSG00000262355 ENST00000305831 ENSTGUG00000013086 > ENSMUSG00000021838**** > > ENSG00000198888 ENST00000361390 ENSTGUG00000018737 > ENSMUSG00000064341**** > > ** ** > > ** ** > > similarly the 08 server: **** > > ** ** > > > http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&step=4&attributes=homologs_ensembl_gene_id%2Cmouse_ensembl_gene%2Cinter_paralog_zebrafish_ensembl_gene&homolog_filters%5B%5D=with_mmusculus_homolog&homolog_filters%5B%5D=only&homolog_filters%5B%5D=Homolog+filters+Orthologous+Mouse+Genes<http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&step=4&attributes=homologs_ensembl_gene_id%2Cmouse_ensembl_gene%2Cinter_paralog_zebrafish_ensembl_gene&homolog_filters%5B%5D=with_mmusculus_homolog&homolog_filters%5B%5D=only&homolog_filters%5B%5D=Homolog+filter> > **** > > ** ** > > ** ** > > ** ** > > a.**** > > ** ** > > ** ** > > On Mon, Nov 26, 2012 at 9:40 AM, Katleen De Preter < > [email protected]> wrote:**** > > Hi,**** > > **** > > I’m trying to perform cross-species ortholog searches > (mice-human-zebrafish). However, it seems that this option is currently not > working on biomart (website and via R). The same script that previously > worked, is currently not successful. Do you know about this problem?**** > > **** > > Kind regards, > > Katleen De Preter**** > > **** > > **** > > -- > > dr. ir. Katleen De Preter > Center for Medical Genetics Ghent (CMGG) > Ghent University Hospital > Medical Research Building (MRB), > 2nd floor, room 120.038 > De Pintelaan 185, > B-9000 Ghent, Belgium > +32 9 332 5533 (phone) | +32 9 332 6549 (fax) > > http://medgen.ugent.be > [email protected] **** > > **** > > **** > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users**** > > ** ** > ------------------------------ > > Geen virus gevonden in dit bericht. > Gecontroleerd door AVG - www.avg.com > Versie: 2012.0.2221 / Virusdatabase: 2629/5420 - datum van uitgifte: > 11/26/12**** >
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