validation on each of pseudo data sets to generate a null distribution, i.e., the distribution of prediction accuracy from all classifiers developed on all pseudo data sets. The null distribution can then be compared with the distribution of multiple 10-fold cross-validation results derived from the real data set. The degree of chance correlation in prediction can be estimated from the overlap of the two distributions.

Figure 4-4 shows the results of a test for chance correlation of a DF classifier to predict the prostate cancer. The distribution of prediction accuracy of the real data set centers around 95% while the pseudo data sets are near 50%. The real data set has a much narrower distribution compared to the pseudo data sets, indicating that the classifiers generated from the cross-validation procedure for the real data set give consistent and high prediction accuracy. In contrast, as expected, the prediction results for the pseudo data sets varied widely, implying a large variability of signal/noise ratio across these pseudo classifiers. Importantly, there is no overlap between two distributions, indicating that a statistically and biologically relevant DF classifier can be obtained using the real data set.

FIGURE 4-4 Prediction distribution in 2,000 runs of 10-fold cross-validation process: (A) real data set and (B) 2,000 pseudo data set generated from a randomization test. Source: Tong et al. 2004.



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