[BioC] beadarray illumina Human610-Quadv1_B.bpm

[Matthew Ritchie]

Hi Nolwenn,

The crlmm package should be able to handle your 610k quad data.

You'll need idat files rather than bead-level text files to get started. 
Take a look at the crlmmIllumina vignette for further information

BTW, the human610quadv1bCrlmm package is a chip-specific package which
contains parameters used internally by crlmm - it isn't really an
annotation package.

I hope this helps.  Best wishes,

Matt

> 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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