[BioC] Fwd: GWASdata

[NAOMI S ALTMAN]

Thanks, Stephanie.

I am not sure how often things gets updated, but a statement to this 
effect in the GWASdata documentation  would be useful.

I am just using the data to learn how to use GWAStools, as well. But 
using both sets of data together seemed "obvious" and that is how I ran 
into trouble.

--Naomi



On 4/16/2014 11:15 AM, Stephanie M. Gogarten wrote:
> 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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