Table 2

Empirical levels for different nominal alpha levels (0.01 and 0.05) using different reference data sets
Strategya Referenceb Modelc α = 0.05d α = 0.01e
MA-pointwise - fixed 0.047 0.009
- random 0.037 0.006
MA-proxy ideal fixed 0.046 0.009
random 0.036 0.007
incomplete fixed 0.046 0.009
random 0.036 0.006
mismatched fixed 0.047 0.009
random 0.036 0.007
MA-impute ideal fixed 0.042 0.007
random 0.035 0.006
incomplete fixed 0.041 0.007
random 0.034 0.006
mismatched fixed 0.039 0.008
random 0.032 0.006

aEnumeration using either the naive approach, proxy algorithm or imputation strategy.

bReference data set used for proxy algorithm and imputation.

cCalculation of the allelic effects by the fixed effect or random effect model.

dEmpirical levels for nominal α of 0.05 (average over all SNPs from chr 22 for 100 permutation replicates).

eEmpirical levels for nominal α of 0.01.

Meesters et al.

Meesters et al. BMC Bioinformatics 2012 13:231   doi:10.1186/1471-2105-13-231

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