[BioC] Illumina BeadArray Annotation

[Simon Lin]

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 at 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