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Table 2 Concordance of calls between batch compositions

From: Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

Comparison BC1 vs BC2 BC1 vs BC3 BC2 vs BC3
Successful Calls for Both SNPs 134128046 134063768 134107787
  % 99.241 99.194 99.226
Concordant Calls (All) SNPs 134109060 134036623 134095792
  % 99.986 99.980 99.991
Concordant Calls (Hom) SNPs 98050788 97992008 98016851
  % 99.989 99.983 99.993
Concordant Calls (Het) SNPs 36058272 36044165 36078941
  % 99.977 99.970 99.985
  1. Successful calls for both: genotype successfully called in both of the compared experiments; Concordant calls (All): same genotype called in both of the compared experiments; Concordant calls (Hom): homozygous genotype called in both of the compared experiments; Concordant calls (Het): heterozygous genotype called in both of the compared experiments.