Hi all, I did a biomaRt query with the most recent package and R2.10. Although my query involves 3 Agilent (mouse) probes, I get results for 2 probes. This is consistent, also with other probes? The code is pasted below. Can anybody give support on this trivial question. Thank you, Patrick > AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051") > Agilent<-getGene(AgiIDs, type = 'agilent_wholegenome', mart=ensembl) > Agilent agilent_wholegenome mgi_symbol description 1 A_51_P183051 Upb1 ureidopropionase, beta Gene [Source:MGI Symbol;Acc:MGI:2143535] 2 A_52_P330395 Farp1 FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived) Gene [Source:MGI Symbol;Acc:MGI:2446173] chromosome_name band strand start_position end_position ensembl_gene_id 1 10 C1 1 74869656 74904424 ENSMUSG00000033427 2 14 E5 1 121434422 121682966 ENSMUSG00000025555 Patrick De Boever, PhD, MSc Flemish Institute for Technological Research (VITO) Unit Environmental Risk and Health, Toxicology group Industriezone Vlasmeer 7, 2400 Mol, Belgium Tel. + 32 14 33 51 45 Fax. + 32 14 58 05 23 patrick.deboever@vito.be<mailto:patrick.deboever@vito.be> Visit our website: www.vito.be/english<http: www.vito.be="" english=""> Uniting expertise from different fields of technology in a pleasant and stimulating environment enhances innovation and the development of novel methods for sustainable production. Have a look at the international congress 'Innovation for Sustainable Production 2010' April, 18-21, 2010 - Bruges (Belgium) http://www.i-sup2010.org --- This e-mail, any attachments and the information it contains are confidential and meant only for the use of the addressee(s) only. Access to this e-mail by anyone other than the addressee(s) is unauthorized. If you are not the intended addressee (or responsible for delivery of the message to such person), you may not use, copy, distribute or deliver to anyone this message (or any part of its contents) or take any action in reliance on it. In such case, you should destroy this message and notify the sender immediately. If you have received this e-mail in error, please notify us immediately by e-mail or telephone and delete the e-mail from any computer. All reasonable precautions have been taken to ensure no viruses are present in this e-mail and its attachments. As our company cannot accept responsibility for any loss or damage arising from the use of this e-mail or attachments we recommend that you subject these to your virus checking procedures prior to use. [[alternative HTML version deleted]]

Patrick have you checked the sequence of the probe A_51_P227502 and aligned (e.g. 'blasted') it against the genome? One possible explanation for what you see is that (with current genome build and annotation) Ensembl might no longer link this probe to a mouse gene. Best wishes Wolfgang De Boever Patrick ha scritto: > Hi all, > > I did a biomaRt query with the most recent package and R2.10. > Although my query involves 3 Agilent (mouse) probes, I get results for 2 probes. This is consistent, also with other probes? > The code is pasted below. > Can anybody give support on this trivial question. > > Thank you, > > Patrick > > >> AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051") >> Agilent<-getGene(AgiIDs, type = 'agilent_wholegenome', mart=ensembl) >> Agilent > agilent_wholegenome mgi_symbol description > 1 A_51_P183051 Upb1 ureidopropionase, beta Gene [Source:MGI Symbol;Acc:MGI:2143535] > 2 A_52_P330395 Farp1 FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived) Gene [Source:MGI Symbol;Acc:MGI:2446173] > chromosome_name band strand start_position end_position ensembl_gene_id > 1 10 C1 1 74869656 74904424 ENSMUSG00000033427 > 2 14 E5 1 121434422 121682966 ENSMUSG00000025555 > > > Patrick De Boever, PhD, MSc > Flemish Institute for Technological Research (VITO) > Unit Environmental Risk and Health, Toxicology group > Industriezone Vlasmeer 7, 2400 Mol, Belgium > Tel. + 32 14 33 51 45 > Fax. + 32 14 58 05 23 > patrick.deboever at vito.be<mailto:patrick.deboever at="" vito.be=""> > > Visit our website: www.vito.be/english<http: www.vito.be="" english=""> > > > > Uniting expertise from different fields of technology in a pleasant and stimulating environment enhances innovation and the development of novel methods for sustainable production. > Have a look at the international congress 'Innovation for Sustainable Production 2010' > April, 18-21, 2010 - Bruges (Belgium) > http://www.i-sup2010.org > --- > This e-mail, any attachments and the information it contains are confidential and meant only for the use of the addressee(s) only. Access to this e-mail by anyone other than the addressee(s) is unauthorized. If you are not the intended addressee (or responsible for delivery of the message to such person), you may not use, copy, distribute or deliver to anyone this message (or any part of its contents) or take any action in reliance on it. In such case, you should destroy this message and notify the sender immediately. If you have received this e-mail in error, please notify us immediately by e-mail or telephone and delete the e-mail from any computer. > All reasonable precautions have been taken to ensure no viruses are present in this e-mail and its attachments. As our company cannot accept responsibility for any loss or damage arising from the use of this e-mail or attachments we recommend that you subject these to your virus checking procedures prior to use. > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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/contact