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
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.
Sean
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
