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Table 3 Comparison of Birdseedv2 results on the basis of Mendelian inheritance pattern

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

Original

Spatial normalization

 

Consistent

Inconsistent

Missing

Consistent

26,877,547

(98.8)

2,969

(0.011)

35,887

(0.13)

Inconsistent

4,765

(0.018)

137,146

(0.50)

2,615

(0.010)

Missing

69,733

(0.26)

2,083

(0.008)

65,255

(0.24)

  1. Entries are frequencies (percentages) of SNP trios from 90 CEU samples of Set 2 (see Method Section). 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 = 20.4 for consistent versus inconsistent; ii.) z = 104.1 for consistent versus missing; and iii.) z = 7.75 for inconsistent versus missing.
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BMC Bioinformatics

ISSN: 1471-2105

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