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

BMC Bioinformatics

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

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.

ISSN: 1471-2105