[BioC] SNPs data analysis

[Matt Ritchie]

Dear Mondher,

I'd suggest you try using beadarraySNP.  The beadarray package doesn't
currently support BeadStudio output from Illumina's genotyping arrays.  It
will read in BeadStudio output from Illumina's expression arrays, and can
handle raw bead-level data (text files and tiffs) for single-channel
(expression) and two-colour (genotyping and methylation) BeadArrays.

Best wishes,

Matt

> Mondher
> 
> For CNV analysis you might also want to look at the beadarraySNP package, and
> the paper cited in the vignette for beadarraySNP.
> 
> Richard.
> 
> Herve Pages wrote:
>> Hi Mondher,
>> 
>> A good start is to read the documentation available in the package.
>> For example you can download the PDF files available on this page:
>> 
>>   http://bioconductor.org/packages/2.3/bioc/html/beadarray.html
>> 
>> or open them directly from your R session with openVignette() (after you've
>> managed to install and load the package). We call these documents
>> vignettes:
>> they generally contain examples (with code) on how to use the package. They
>> are a great way to learn how to use it. Then when it's time to dive into
>> the gory details of how to use a particular function, '?somefuntion'
>> is your friend, especially the example section.
>> 
>> Ask here again if you have a more specific questions about the package.
>> 
>> Good reading!
>> H.
>> 
>> 
>> Mondher GATRI wrote:
>>> Dear All,
>>> 
>>> I'm Mondher Gatri, I'm working at EPFL, Switzerland. during my work
>>> I'm dealing with SNPs datasets. I would like to use BeadArray to
>>> normalize BeatStudio SNPs data. Would you please inform me about how
>>> to use beadarray package for normalization, quality control and CNV
>>> computing.
>>> 
>>> Kink regards,
>>> Mondher


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