[BioC] Manufacturer ids in lumiHumanV1

[Pan Du]

Hi Benjamin

There are potential problems of directly using Illumina Target identifier or
probe identifier because of its imperfect design. For example, there are
duplicated Target IDs in the same chip. The same probe can have different
Target IDs. The nuID is designed to solve these problems. It can be directly
convert to the probe sequence and get the latest annotation easily. Also,
the annotation packages like lumiHumanV1 provides the mapping between
TargetID to nuID and probe Id to nuID.

Please check the vignette of lumi package and the paper published in Biology
Direct 2007, 2:16:
nuID: a universal naming scheme of oligonucleotides for Illumina,
Affymetrix, and other microarrays

Tell me if you have any questions.

Pan



On 7/6/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> ------------------------------
> 
> Message: 2
> Date: Thu, 5 Jul 2007 13:00:14 +0200
> From: "Benjamin Otto" <b.otto at uke.uni-hamburg.de>
> Subject: [BioC] Manufacturer ids in lumiHumanV1
> To: "BioClist" <bioconductor at stat.math.ethz.ch>
> Message-ID: <000901c7bef3$ac604870$9f05a20a at matrix.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear bioconductors,
> 
> I just installed the lumiHumanV1 package via the biocLite() procedure
> yesterday. The identifiers of the single probes look very strange to me.
> Beside that they don't appear  in the annotation file provided by Illumina
> the name composition itself made me, let me say somehow suspicious! Here
> comes a quick extract. Did someone observe that before?