Dear all, My apologies, the annotation problem was not with biomaRt, but with the prepackaged datasets: 1. lumiHumanIDMapping.db and 2. lumiMouseIDMapping.db. The description of the problem remains the same, though. Gioulietta and Wolfgang, thank you for the prompt reply. Regards, Nenad p.s. The missing sessionInfo(): R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] lumiMouseIDMapping.db_1.0.0 lumiHumanIDMapping.db_1.0.0 [3] lumi_1.8.3 RSQLite_0.7-1 [5] preprocessCore_1.4.0 mgcv_1.4-1.1 [7] affy_1.20.2 annotate_1.20.1 [9] xtable_1.5-4 AnnotationDbi_1.4.2 [11] RMySQL_0.7-2 DBI_0.2-4 [13] biomaRt_1.16.0 R.utils_1.1.1 [15] R.oo_1.4.6 R.methodsS3_1.0.3 [17] Biobase_2.2.1 loaded via a namespace (and not attached): [1] RCurl_0.94-0 XML_1.99-0 affyio_1.10.1 >> Hi Nenad, >> >> I had a look at our BioMart interface- the web interface at: >> >> www.ensembl.org/biomart/martview >> >> It appears to me that the Illumina V1 probe set attribute for mouse >> gives the correct probe names. I believe the Illumina V1 set for >> mouse >> is the same as MouseWG6_V1. >> >> If you give me more details (i.e. which genes you are looking at, or >> which filters you applied) I can give this another try. At first >> glance, it doesn't look like an Ensembl data problem. >> >> Regards, >> Giulietta (Ensembl Helpdesk) >> >> >> On Tue Feb 17 13:35:57 2009, huber@ebi.ac.uk wrote: >>> Hi Nenad >>> >>> thank you for reporting this! >>> >>> Since your question raises a more general operational question with >>> biomaRt, I'd like to use the opportunity to explain, to this list, >>> what's going on (not quite) behind the scenes. There are three >>> separate >>> organisations involved in this information chain: >>> >>> 1. The Ensembl database team (in Cambridge UK) >>> >>> 2. The BioMart software developers (in Toronto CA) and Rhoda >>> Kinsella >>> (in Cambridge) who imports the Ensembl data into the BioMart system >>> >>> 3. Bioconductor and specifically the biomaRt R package, which is >>> simply >>> a thin interface from R to a webservice, with no own content or >>> logic >>> (maintained Steffen Durinck in sunny Berkeley.) >>> >>> Questions at levels 2 and 3 are good to ask on this list and are >>> usually >>> efficiently answered e.g. by Steffen or Rhoda. >>> >>> What you report is, afaIct, an Ensembl data content problem, i.e. >>> level >>> 1. Here the advise is to email the Ensembl help desk: >>> helpdesk@ensembl.org >>> >>> I hope this helps, please let us know if you have any more questions >>> or >>> observations. >>> >>> Best wishes >>> Wolfgang >>> >>> ---------------------------------------------------- >>> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber >>> >>> >>> -------- Original Message -------- >>> Subject: [BioC] Reporting problem with annotation in biomaRt, >>> Illumina >>> arrays >>> Date: Tue, 17 Feb 2009 12:02:37 +0000 >>> From: Nenad Bartonicek <nenad@ebi.ac.uk> >>> To: bioconductor@stat.math.ethz.ch >>> >>> Dear all, >>> >>> There seems to be a problem with probe annotation of certain >>> Illumina >>> arrays in biomaRt. >>> >>> The following arrays: HumanWG6_V1, HumanRef8_V1, MouseWG6_V1, >>> MouseWG6_V1_B do not have valid Illumina probe names under the >>> "ProbeId" column. >>> They seem to contain values which are in the column >>> "Array_Address_Id", which is the one next to the Probe_id column in >>> the official Illumina flat files. >>> >>> For example. the array "MouseWG6_V1" >>> >>> library(lumiMouseIDMapping.db) >>> dbconn=lumiMouseIDMapping_dbconn() >>> tableNames=dbListTables(lumiMouseIDMapping_dbconn()) >>> tableNames = tableNames[grep("Mouse",tableNames)] >>> tableNames >>> data = dbReadTable(dbconn,"MouseWG6_V1") >>> head(data) >>> >>> The column ProbeId contains identifier "105290026" which is in the >>> flat file on >>> http://www.switchtoi.com/pdf/Annotation%20Files/Mouse/MouseWG- >>> 6_V1_1_R4_11234304_A.zip >>> under the column Array_Address_Id and has a proper identifier of >>> "ILMN_1229450". >>> >>> Hope this helps and that it might be corrected sometime in the >>> future, >>> >>> Nenad >>> >>> Nenad Bartonicek >>> EMBL- European Bioinfromatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> [[alternative HTML version deleted]]