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Table 2 Contrasting Birdseedv2 results in Table 1 using 32,752 non-missing consensus HapMap calls

From: Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays

Original Spatial normalization
  Agree Disagree Missing
Agree - 1,176
(3.6)
7,690
(23.5)
Disagree 2,518
(7.7)
7
(0.02)
2,716
(8.3)
Missing 16,887
(51.6)
1,758
(5.4)
0
  1. Entries are frequencies (percentages) out of the 32,752 genotypes. Agreement and disagreement are with respect to the non-missing consensus HapMap calls. Separate one tailed McNemar's tests on the three pairs of discordant entries suggest significant improvement in favor of the use of spatial normalization: i.) z = 22.1 for agree versus disagree; ii.) z = 58.7 for agree versus missing; and iii.) z = 14.3 for disagree versus missing.