[BioC] About Lumi nuID NAs

[Pan Du]

Hi Simone,

The reason of NAs is that the annotation packages are only based on the
RefSeq Ids. However, when Illumina designed the chips, lots of probes are
based on other sequence information instead of using RefSeq. To solve the
problem, we have Blasted all the probe sequences against most recent RefSeq
database. The result is already in the nuID website (
http://www.basic.northwestern.edu/nuID/) . We will package them for the next
release of Bioconductor annotation packages. An alternative is to directly
use the Illumina annotation which is included in the featureData of the
LumiBatch object if you use the recent lumi (>1.5.14) to input the data
(suppose the BeadStudio outputted the annotation information). Tell me if
you have further questions. Thanks.


Pan


On 2/21/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 15
> Date: Wed, 20 Feb 2008 22:51:34 +0100
> From: "Simone de Jong" <s.dejong-6 at umcutrecht.nl>
> Subject: [BioC] Lumi nuID NA
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <001301c8740a$c3e0be40$4aa32f0a at cog063>
> Content-Type: text/plain
> 
> Hi, 
> 
>  
> 
> I've been working with lumi to preprocess my data. This has been working
> really well. However, I'm experiencing some difficulties with the nuID
> functions. 
> 
>  
> 
> I've annotated my data with the LumiMouseV1 library, but there seem to be a
> lot of NA's when looking up symbols, NM numbers, anything. The most
> confusing part is that I also get NA's when using nuID2target
> ID or nuID2probeID.
> 
>  
> 
> I've tried it the other way around, annotating the Illumina TargetID's by
> targetID2nuID and that gives me a complete list. The nuIDs of the genes,
> however, that were NA when mapping to targetIDs do not appear in that list.
> 
>  
> 
> Does anybody know why this happens and how I can solve it?
> 
>  
> 
> Thanks,
> 
> Simone
> 
>  
> 
> ___________________
> 
> Simone de Jong, Msc.
> 
> PhD student
> 
> The Netherlands