[BioC] GWASdata

[Naomi Altman]

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