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Table 3 Comparing accuracy of allele frequency estimates from different reference samples for 500 k platform (1).

From: Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction

Actual AF compared with: Correlation MAD error (95% CI)
AF estimates from 500 k Sample Data Set Cases 0.909 0.079 (0.1015-0.1020)
  Controls 0.907 0.079 (0.1024-0.1029)
AF estimates from individually typed samples Cases 0.987 0.035 (0.0389-0.0391)
  Controls 0.985 0.037 (0.0411-0.0414)
  1. Actual allele frequencies obtained from individual genotyping of the 1st set of 60 case and 60 control samples were compared with estimated allele frequencies of the same set 120 samples. Estimated allele frequencies were separately calculated using beta values obtained from the 500 k Sample Data Set, and from the individually genotyped samples on the 500 k array.