naomi at stat.psu.edu
Mon Apr 14 20:15:54 CEST 2014
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?
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