I've had success with GWASTools and Affy SNP 6.0. The GWASTools authors 
have written a detailed tutorial that describes their approach to data 
cleaning and quality control. It can be found here:

http://www.bioconductor.org/packages/release/bioc/vignettes/GWASTools/inst/doc/DataCleaning.pdf

Cheers,
Fred

On 6/3/12 6:04 PM, Vincent Carey wrote:
> There are various ways of proceeding.  For calling with crlmm, an example
> of a full analysis is given with
>
> http://www.bioconductor.org/packages/2.10/bioc/vignettes/crlmm/inst/doc/gtypeDownstream.pdf
>
> be sure to look at
>
> http://www.bioconductor.org/packages/2.10/bioc/html/crlmm.html
>
> GWASTools should also be consulted.
>
> On Sun, Jun 3, 2012 at 6:52 PM, David Hervás<ddhervas@yahoo.es>  wrote:
>
>> Hello,
>>
>> I'm new to Bioconductor and after searching and reading lots of
>> documentation files from different packages I still haven't figured how to
>> perform GWAS with Affymetrix SNP 6.0 arrays
>> As far as I know I need "oligo", "pd.genomewidesnp.6" and "snpStats"
>> pacakages but I haven't found an example of how to put all the commands
>> together.
>>
>>
>> I've managed to read my .CEL files with the following code provided in the
>> oligo package documentation:
>>
>> setwd("d:\\CELS\\")
>> fullFilenames<- list.celfiles(full.names=TRUE)
>> outputDir<- file.path(getwd(), "crlmmResults")
>>
>> if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir)
>>
>> crlmmOut<- getCrlmmSummaries(outputDir)
>>
>>
>> I get a SnpSuperSet object, and I also know how to get the genotypes from
>> it with
>>
>> genotype<-calls(crlmmOut)
>>
>> What are the next steps to perform the association analysis? Documentation
>> in oligo package suggests "snpStats" but I have no idea how to make this
>> package read my SnpSuperSet object or my genotype matrix, since snpStats
>> needs a SNPmatrix object. I've also tried other packages but none seem to
>> be able to read SnpSuperSet objects.
>>
>> Thanks in advance for you help
>>
>>
>> ________________
>> David Hervás Marín
>> Biostatistician in IIS La Fe - Valencia
>>
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>>
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