Illumina BeadArray Annotation
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Simon Lin ▴ 270
@simon-lin-1272
Last seen 9.6 years ago
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
Annotation Cancer lumiMouseV1 lumi trigger Annotation Cancer lumiMouseV1 lumi trigger • 914 views
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