[BioC] beadarray illumina Human610-Quadv1_B.bpm

[Mark Dunning]

I think the annotation package you want is human610quadv1bCrlmm which
works with the crlmm package.

beadarray doesn't support SNP arrays very well at the moment although
we plan to do something about that for future releases.

Best,

Mark

On Wed, Apr 28, 2010 at 5:13 PM, Nolwenn Le Meur <nlemeur at irisa.fr> wrote:
> Hi everyone,
>
> I am trying to analyse illumina SNP array for GWAS but (as many of you) I
> have annotation problems.
> The experiment files are not recent and the chip type is  Human610-Quadv1_B.
>  Does that correspond to the illuminaHumanv1.db for annotation?
>
> I have tried to use the Humanv1 annotation with the readIllumina() function
> of the beadarray package but it seems not to be recognized by the next
> functions I use in my analysis (e.g. createBeadSummaryData)
>
> Here is for example the header of one of my txt files with measurements :
>
> Code    Grn     GrnX    GrnY    Red     RedX    RedY
> 10600301        2850    886.7655        7162.112        2645    901.0966
>    7157.959
> 10600301        2256    1402.927        1904.34 2426    1417.054
>  1900.684
> 10600301        2425    1112.202        5480.152        2405    1126.806
>    5476.067
>
> and the annotation file I have in hand (also txt)
>
> Human610-Quadv1_B.bpm.Address   Name    Chr     Position
> 10600301        rs10000010      4       21227772
> 10600305        rs10006395      4       6913032
> 10600309        rs10006554      4       168208659
>
> Any help is appreciated.
>
> Nolwenn Le Meur
>
> IRISA Symbiose D151
> Université de Rennes I
> Campus Beaulieu
> 35042 Rennes Cedex
> France
> Phone: +33 2 99 84 71 17
> Fax: +33 2 99 84 71 71
> E-mail: nlemeur at irisa.fr
> Web: http://www.irisa.fr/symbiose/nolwenn_le_meur
>
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