Figure 3

Prediction interval under the null hypothesis of no association. Quantile-quantile (QQ) prediction intervals for 1,000 permutations of the case–control status. The λ-value represents the median (2.5 percentile to 97.5 percentile) of all genomic inflation factors λ. (A) Quantile normalisation and adjustment for control probe PCs. Under no association we observe and overall statistical deflation, but also a high degree of statistical inflation for a small number of permutations. (B) Quantile normalisation, adjustment for control probe PCs, gender, age, white blood cells and PC1-5. Adjustments abolishes overall statistical deflation and results in a substantially more narrow prediction interval.