[BioC] Illumina BeadArray Annotation

Simon Lin simonlin at duke.edu
Tue May 22 23:57:23 CEST 2007

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 
4) The potnetially cross-hybrdized probes are identified and documented.



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 at uq.edu.au>
Subject: Re: [BioC] LumiMouseV1 error
To: "Shawn Westaway" <westaway at ohsu.edu>
Cc: bioconductor at stat.math.ethz.ch
<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)


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