Table 1

Reliability of allele frequency estimates in DNA pools for SNPs on the Affymetrix 500 K microarray.

Array

All SNPs

MAF > .05

Worst

Best

Average

Worst

Best

Average


NspI (250 k)

0.952 (0.069)

0.969 (0.056)

0.957 (0.063)

0.934 (0.072)

0.963 (0.058)

0.947 (0.065)

StyI (250 k)

0.944 (0.075)

0.968 (0.067)

0.955 (0.070)

0.944 (0.079)

0.964 (0.070)

0.949 (0.073)

Both (500 K)

0.949 (0.071)

0.962 (0.062)

0.956 (0.066)

0.94 (0.075)

0.956 (0.065)

0.948 (0.069)


Values are mean Pearson correlation coefficients (r) between the 5 DNA pools using the average of all quartet estimates (RASav-all). 'Worst' and 'Best' refer to the 10 bivariate comparisons between the 5 DNA pools and 'Average' is the average of these 10 correlations. Values in parentheses are mean absolute differences between DNA pools. 'All SNPs' includes all SNPs on the array (including rare and non-polymorphic SNPs) for which 70% of quartet measurements were available (N = 457,607 – 487,666 across both microarrays). 'MAF > .05' only includes SNPs with minor allele frequency greater than .05 (N = 428,179 – 456,241 across both microarrays).

Docherty et al. BMC Genomics 2007 8:214   doi:10.1186/1471-2164-8-214

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