[BioC] New version of BeadStudio - new Illumina data files

[Pan Du]

Hi Ingrid,

You can use "Sample Probe Profile.txt", which provides probe ID, then you
can still use lumi annotation packages (named like lumiHumanV2). We plan to
release annotation packages based on latest BLAST result at the beginning of
next year.


Pan


On 12/7/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 4
> Date: Thu, 6 Dec 2007 16:51:35 +0100
> From: Ingrid H. G. ?stensen  <Ingrid.H.G.Ostensen at rr-research.no>
> Subject: [BioC] New version of BeadStudio - new Illumina data files
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <AFE5B2464F1EB547BBACE62CCE8E40200B81D0 at mr3k6001.ad.medicalresearch.no>
> 
> Content-Type: text/plain
> 
> Hi
> 
> With the new version of BeadStrudio (v 3.2) a new manifest file has been
> introduced:  HumanWG-6_V2_0_R1_11223189_A.bgx. If one uses this one the target
> id is no longer ILMN_‰a number‰ but a mix of gene symbol, other official
> identifiers and other identifiers. Using the output files made with the new
> version makes it „impossible‰ to annotate or GO classify the data using
> R/BioC, probably because of the change in target id.
> 
> Are there any plans of updating the packages that are to be used with Illumina
> data? 
> 
> Does any one have any plans of making annotation files (and similar) that can
> be used on
> the probe profile files?
> 
> Regards,
> Ingrid
> 
>