Table 2

False Positive Rate of Matched and PC adjusted Unmatched GWAS

Scenario

Cases/Controls

False Positive Rate*


Matched

2000/2000

5.00E-07

Unmatched + PCs

2000/2000

8.00E-07

Unmatched + PCs

2000/2250

9.00E-07

Unmatched + PCs

2000/2500

1.30E-06

Unmatched + PCs

2000/2750

1.20E-06

Unmatched + PCs

2000/3000

9.00E-07

Unmatched + PCs

2000/3250

1.00E-06

Unmatched + PCs

2000/3500

8.00E-07

Unmatched + PCs

2000/3750

9.00E-07

Unmatched + PCs

2000/4000

8.00E-07


*False positive rate with a p-value cut-off of 1E-06

We report the false positive rate of a matched GWAS and compare it to PC-adjusted unmatched GWASs with varying number of controls. The false positive rate is computed using a p-value cut-off of 1E-06.

Solovieff et al. BMC Genetics 2010 11:108   doi:10.1186/1471-2156-11-108

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