[BioC] Fwd: GWASdata

[Stephanie M. Gogarten]

Hi Naomi,

Sorry for the delay in responding, I was traveling.  The GWASdata 
package was made for the sole purpose of running examples for the 
GWASTools package, so I would be wary of using it for any other 
purposes.  I think the Affy and Illumina data sets are not using the 
same A/B coding scheme, so switching A and B for the entire data set 
will not work - some SNPs will need to be flipped and some will not. 
Unfortunately the Affy data does not have annotation for the alleles 
used (I inherited the example data from someone else several years ago, 
and it didn't come with annotation then).

The Illumina data does have allele annotation, so you could compare 
those samples with 1000 genomes data if you want to investigate SNP 
concordance methods.

Stephanie

On 4/15/14 8:37 AM, Vincent Carey wrote:
> It did go through.  I am not too familiar with these packages.  You might
> check the 1000 genomes calls to get a third vote, as at least some of the
> samples
> should be present in the 1000 genomes VCF.
>
>
> On Tue, Apr 15, 2014 at 8:11 AM, Naomi Altman <naomi at stat.psu.edu> wrote:
>
>> This did not seem to go through the first time. --Naomi
>>
>>
>> -------- Original Message --------
>> Subject:        GWASdata
>> Date:   Mon, 14 Apr 2014 14:15:54 -0400
>> From:   Naomi Altman <naomi at stat.psu.edu>
>> To:     Bioconductor mailing list <bioconductor at r-project.org>
>>
>>
>>
>> I have been trying out some of the SNP tools using the GWASdata data
>> sets.  One thing I did was to look for differences in genotype calls
>> between the Affy and Illumina data for what appear to be the same
>> subjects (they have the same subject and family id).  They are highly
>> discrepant.  At first I thought that the A and B alleles were switched,
>> but swopping the 0's and 2's did not change the magnitude of number of
>> discrepancies.  The SNPs appear to be in the same order.
>>
>> Have I misinterpreted something?
>>
>> --Naomi
>>
>>
>>
>>
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