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Hi Ingrid, Thanks for letting me know about the change. I will use the most current identifiers in the next release of the annotation package. I have already have annotation packages for the probe identifiers. I can put them on a temporary ftp site if you are interested. Lynn Ingrid H. G. ?stensen wrote: > 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 > > > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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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 > >