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 at 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 at 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 at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor