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Table 1 Comparing estimated and actual allele frequencies in sub-pools for 500 k platform.

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)
Case Pool 1 0.981 0.042 (0.0461-0.0463)
Case Pool 2 0.982 0.041 (0.0451-0.0453)
Case Pool 3 0.975 0.049 (0.0536-0.0540)
Average of Case Pools 0.987 0.035 (0.0389-0.0391)
Control Pool 1 0.977 0.044 (0.0496-0.0499)
Control Pool 2 0.976 0.049 (0.0526-0.0529)
Control Pool 3 0.978 0.046 (0.0501-0.0504)
Average of Control Pools 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 from pooled genotyping of the same 120 samples. The comparison was carried out for samples in each of the sub-pools, and for averaged allele frequencies across the 3 sub-pools.