On Wed, Apr 28, 2010 at 12:13 PM, Nolwenn Le Meur <nlemeur@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?
>
>
illuminaHumanv1.db is for the "v1" illumina bead arrays for gene expression
measurement


> 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 :
>
>
have you looked at the beadarraySNP package?  there is a vignette.



> 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@irisa.fr
> Web: http://www.irisa.fr/symbiose/nolwenn_le_meur
>
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