[BioC] Problems with lumiR/lumiMouseV1

[Cei Abreu-Goodger]

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.