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The threshold hook and the horizontal line provide the true and the apparent (false) thresholds for good RNA quality in terms of the logged 3′/5′-intensity ratios, Δ3′/5′ < Δthreshold.
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Finally, permutation and resampling methods also provide empirical estimates for false discovery thresholds [ 74, 79].
This clinical observation excluded the need to estimate multiple testing and false discovery thresholds for SOX9, a common strategy undertaken for candidate selection in high-throughput studies.
The ROC curves from the final model (Fig. 2) provide practical guides for the choices between desired false positive thresholds (1-specificity) and expected true positive rates (sensitivity) for predicting all color categories.
Previously the threshold for significance, taking false discovery threshold into account, has been set to B>0 for this type of tissue and microarray [7], [19], [41].
After collecting the 50 p-values, the true positive rate corresponding to a given false positive threshold was estimated as the proportion of simulations identifying the true positive gene using the false positive threshold.
This model was inferior to the full model, with an AUC of 0.60 and 42% true positive rate at the 30% false positive threshold ('Basic model' in Fig. 3).
At a 1% false positive threshold 1863 nonredundant proteins or protein groups were identified.
The data from the simulations were used to calculate the true positive rate based on a given false positive threshold.
Due to the fixed false discovery threshold centroid probe numbers differed between data sets.
We corrected for multiple testing with a false discovery threshold of P < 0.05.
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