Hello all, I saw a couple of emails on the list with this problem regarding Illumina BeadChip Mouse-6 data. My problem is that for some probes I end up with only a nuID, with no mapping to the manufacturer's TargetID or ProbeID, and no transcript annotation. In some cases the annotation file from Illumina's web page would allow me to fill in this missing annotation, but it becomes very tedious since I don't have the TargetID or ProbeID. Does someone know if there is an update to lumiMouseV1 planned? Thanks, Cei --- output --- > rawLumi <- lumiR(fileName, detectionTh = 0.95, lib = 'lumiMouseV1') Loading required package: lumiMouseV1 Warning messages: 1: Some identifiers cannot be found in the lumiMouseV1! in: addNuId2lumi(x.lumi, lib = lib) 2: Duplicated IDs found and were merged! in: addNuId2lumi(x.lumi, lib = lib) -- sessionInfo -- > sessionInfo() R version 2.5.1 (2007-06-27) x86_64-unknown-linux-gnu locale: C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: lumiMouseV1 lumi annotate mgcv affy affyio "1.2.0" "1.2.0" "1.14.1" "1.3-25" "1.14.2" "1.4.1" Biobase "1.14.1" -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

I just realized that the "Gene_Profile" files do not have this issue, only the "Probe_Profile" files. I imagine most of the annotation is done at the Gene level. But I'm particularly interested in the transcript assignments, which could vary. Any thoughts? Thanks, Cei Cei Abreu-Goodger wrote: > Hello all, > > I saw a couple of emails on the list with this problem regarding Illumina > BeadChip Mouse-6 data. My problem is that for some probes I end up with > only a nuID, with no mapping to the manufacturer's TargetID or ProbeID, > and no transcript annotation. In some cases the annotation file from > Illumina's web page would allow me to fill in this missing annotation, but > it becomes very tedious since I don't have the TargetID or ProbeID. > > Does someone know if there is an update to lumiMouseV1 planned? > > Thanks, > > Cei > > --- output --- > > >> rawLumi <- lumiR(fileName, detectionTh = 0.95, lib = 'lumiMouseV1') >> > Loading required package: lumiMouseV1 > Warning messages: > 1: Some identifiers cannot be found in the lumiMouseV1! in: > addNuId2lumi(x.lumi, lib = lib) > 2: Duplicated IDs found and were merged! in: addNuId2lumi(x.lumi, lib = > lib) > > -- sessionInfo -- > > >> sessionInfo() >> > R version 2.5.1 (2007-06-27) > x86_64-unknown-linux-gnu > > locale: > C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > > other attached packages: > lumiMouseV1 lumi annotate mgcv affy affyio > "1.2.0" "1.2.0" "1.14.1" "1.3-25" "1.14.2" "1.4.1" > Biobase > "1.14.1" > > > > > -- Cei Abreu-Goodger, PhD Wellcome Trust Sanger Institute Computational and Functional Genomics Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.