Hi Paul, We are making major overhaul of the annotation workflow. Previously, sequences from the FANTOM database were all reported as NA. To fix the problem, here is the new workflow: 1) The mapping from a 50-mer to a gene is done by BLAST. 2) The most recent release of the RefSeq (this week) is used. 3) We have an automatic trigger of the BLAST when a new verion of RefSeq is out. 4) The potnetially cross-hybrdized probes are identified and documented. Cheers, Simon *************************************************** Simon Lin, MD, CSDP Associate Director, Bioinformatics 676 N Saint Clair, Suite 1200 Robert H. Lurie Comprehensive Cancer Center Northwestern University, Chicago, IL 60611 s-lin2 at northwestern.edu Ph: 312-695-1331 FAX: 772-382-0315 ====================== Date: Fri, 4 May 2007 09:39:45 +1000 From: "Paul Leo" <p.leo@uq.edu.au> Subject: Re: [BioC] LumiMouseV1 error To: "Shawn Westaway" <westaway at="" ohsu.edu=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <de3d1f203daf7a4cb259560d2801df8ba9c6d5 at="" uqexmb2.soe.uq.edu.au=""> Content-Type: text/plain; charset="us-ascii" I have used the lumi package recently and did not get this error (see below). However I did note that the lumi annotation was somewhat incomplete. May of the nuid's just returned "NA" when I asked for the actual annotations (description or LL or SYMBOL). So I also used the Illumina provided annotation file to fill in these gaps. Strangely the web site introducing the NUID's did have actual annotations for some of these problem niud's. So I don't think the lumiMouseV1 on the Bioconductor web site has the latest work??? How does your version differ to what I have used..(see below) Cheers Paul