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Table 1 Concordance of calls between batch sizes

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

Comparison BS1 vs BS2 BS1 vs BS3 BS2 vs BS3
Successful Calls for Both SNPs 134258764 134187584 134265847
  % 99.338 99.285 99.343
Concordant Calls (All) SNPs 134248899 134187584 134253973
  % 99.993 99.986 99.991
Concordant Calls (Hom) SNPs 98179772 98136394 98204063
  % 99.997 99.993 99.995
Concordant Calls (Het) SNPs 36069127 36031744 36049910
  % 99.981 99.964 99.980
  1. Successful calls for both: SNP genotypes 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.