Hi Al, The current version of lumiHumanAll.db was built based on Illumina Company provided annotation files. As the probes were designed based on different sources, lots of probes have no EntrezID available. One option is to blast the probe sequence against the latest human genome to get the mappings. The probe sequence can be easily converted from nuID by id2seq() function in the lumi package. You can also check https://prod.bioinformatics.northwestern.edu/nuID/ , which list the mapping between nuID and corresponding annotations. I am trying to convert these mapping as annotation libraries within next two months. Pan On 6/10/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Tue, 10 Jun 2008 06:40:19 +0100 > From: "Al Ivens" <alicat at="" sanger.ac.uk=""> > Subject: [BioC] lumiHumanAll.db, GOstats > To: "'bioc'" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <00ad01c8cabc$7b2e8d90$5ebcd781 at internal.sanger.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After > linear model fitting and clustering, I have identified a cluster of ~130 > loci that show an interesting profile. However, as 125 of them have no > GeneName or EntrezID, I am struggling to figure out what they might be > biologically. > >> From a closer inspection of lumiHumanALl.db, I find that approx. half of > the features have no EntrezID, so I wasn't just unlucky with the > constituents of my cluster! > > Does anyone have any recommendations as to the best approach to get > around this problem (which came to light when I tried to run GOstats, > which requires EntrezID for mapping of terms)? > > Many thanks in advance. > > Cheers, > > a > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------ Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan at northwestern.edu

Hi Pan, Thanks for your response, had a feeling BLAST was going to be the answer! I'll have a look at the web site first though. Cheers, a > -----Original Message----- > From: Pan Du [mailto:dupan at northwestern.edu] > Sent: 10 June 2008 16:11 > To: bioconductor at stat.math.ethz.ch; alicat at sanger.ac.uk > Subject: Re: [BioC] lumiHumanAll.db, Gostats > > > Hi Al, > > The current version of lumiHumanAll.db was built based on > Illumina Company provided annotation files. As the probes > were designed based on different sources, lots of probes have > no EntrezID available. One option is to blast the probe > sequence against the latest human genome to get the mappings. > The probe sequence can be easily converted from nuID by > id2seq() function in the lumi package. You can also check > https://prod.bioinformatics.northwestern.edu/nuID/ > , which list the mapping between nuID and corresponding > annotations. I am trying to convert these mapping as > annotation libraries within next two months. > > > Pan > > > On 6/10/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" > <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > > > Date: Tue, 10 Jun 2008 06:40:19 +0100 > > From: "Al Ivens" <alicat at="" sanger.ac.uk=""> > > Subject: [BioC] lumiHumanAll.db, GOstats > > To: "'bioc'" <bioconductor at="" stat.math.ethz.ch=""> > > Message-ID: <00ad01c8cabc$7b2e8d90$5ebcd781 at internal.sanger.ac.uk> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > Working with the Illumina Human WG6 chips, and > lumiHumanAll.db. After > > linear model fitting and clustering, I have identified a cluster of > > ~130 loci that show an interesting profile. However, as > 125 of them > > have no GeneName or EntrezID, I am struggling to figure out > what they > > might be biologically. > > > >> From a closer inspection of lumiHumanALl.db, I find that > approx. half > >> of > > the features have no EntrezID, so I wasn't just unlucky with the > > constituents of my cluster! > > > > Does anyone have any recommendations as to the best approach to get > > around this problem (which came to light when I tried to > run GOstats, > > which requires EntrezID for mapping of terms)? > > > > Many thanks in advance. > > > > Cheers, > > > > a > > > > > > > > > > -- > > The Wellcome Trust Sanger Institute is operated by Genome Research > > Limited, a charity registered in England with number 1021457 and a > > company registered in England with number 2742969, whose registered > > office is 215 Euston Road, London, NW1 2BE. > > > ------------------------------------------------------ > Pan Du, PhD > Research Assistant Professor > Northwestern University Biomedical Informatics Center > 750 N. Lake Shore Drive, 11-176 > Chicago, IL 60611 > Office (312) 503-2360; Fax: (312) 503-5388 > dupan at northwestern.edu > ------------------------------------------------------ > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.