Figure 4.

Sensitivity of 1-d.f. association testing methods to clustering quality and differential errors between cases and controls in simulated data. Six alternative association methods are considered: (i) Mann-Whitney testing for difference in location of CNV measurement distributions, (ii) χ² trend tests on data binned with a priori thresholds, (iii) χ² trend tests on mixture model assignment of case and controls together (MM-C), (iv) χ² trend tests on mixture model assignment of case and controls separately (MM-S), (v) χ² trend tests on high confidence mixture model assignment of case and controls separately (MM-S95) and (vi) likelihood ratio trend test. Overdispersion (λ) is estimated robustly from a linear fit to the first 90% of quantile-quantile plots from 1,000 simulated datasets. (a) Overdispersion is estimated for alternative association methods at ten different clustering qualities. Density plots for three clustering qualities are shown at the bottom. (b) Overdispersion is estimated for alternative association methods at ten different values of differential shift of means. Density plots for three values of differential shift are shown at the bottom with case and control groups in red and gray. (c) Overdispersion is shown for alternative association methods at ten different values of differential shifts in variance. Density plots for three values of differential shift are shown at the bottom with case and control groups in red and gray.