[BioC] Quick illumina question

Sean Davis sdavis2 at mail.nih.gov
Tue Jul 25 16:37:46 CEST 2006

Thanks, Lynn, for the offer.  Just to clarify what we do, we actually
reannotate the probes (via blast against refseq, ensembl, dbEST,
unigene_unique, various genome builds, etc.) for all the arrays that we use
and then use a relational database for storing and querying probe
information and annotation.  This gives us mapping information down to the
base pair and the ability to link in any annotation we like, which is often
useful, particularly for sticky issues like probe performance (or lack
thereof) and cross-platform comparisons.

In this particular case, it turns out that the "bead manifest" is the file
that I needed, which Illumina was able to provide via their technical
support after a few directed questions.


On 7/24/06 12:46 PM, "Lynn Amon" <lynnamon at u.washington.edu> wrote:

> I have made annotation packages for the Illumina Refseq beadchips for
> human and mouse.  I submitted these to Bioconductor but I guess they
> didn't make the cut.  The compressed files are 10 MB.  If you are
> interested, I could try emailing them to you.
> Lynn Amon
> Research Scientist
> Department of Pathology
> University of Washington
>> Message: 16
>> Date: Fri, 21 Jul 2006 21:53:41 -0400
>> From: Sean Davis <sdavis2 at mail.nih.gov>
>> Subject: [BioC] Quick illumina question
>> To: Bioconductor <bioconductor at stat.math.ethz.ch>
>> Message-ID: <C0E6FD65.162F%sdavis2 at mail.nih.gov>
>> Content-Type: text/plain; charset="US-ASCII"
>> I have been looking at some raw illumina data.  The results are reported
>> with the illumicode id.  I can't seem to find where I can convert the
>> illumicode to the actual associated sequence.  Can someone who is using
>> illumina arrays point me in the right direction?
>> Thanks,
>> Sean

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