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At each new threshold for probe positivity, the sensitivity and specificity were recalculated.
A similar analysis can be applied to the ratiometric threshold for probe positivity.
The hybridisation intensity threshold for probe exclusion is set arbitrarily and ranges from 0 (no probe selection) to 1000.
Each point on any given ROC curve is the true positive rate (sensitivity) plotted against the false positive rate (1-specificity) resulting from the threshold for probe positivity calculated for a single value.
The threshold for probe expression was set as 11.0 based on the distribution of the intensities of positive and negative control probes, pseudomedian filter setting, and the accuracy of transcript boundary detection.
A statistical threshold for probe positivity of the mean background count rate plus two standard deviations, for example, would reduce the statistical confidence level of a true positive and true negative measurement from a 85.6% probability for three-sigma statistical threshold to a 76.0% probability for the for two-sigma statistical threshold.
Similar(51)
The false positive rate, the fraction of intensities over the threshold for probes specific to a different strain, was only 0.29%.
Differentially regulated genes were identified using a 1.5 fold expression change threshold for probes that passed a significance test up to 360 minutes post-treatment.
We used varying p value thresholds for probe selection due to the absence of probes significant at the 0.05 level.
Thresholds for probe removal were adjusted as proposed in [ 44], see Additional file 1: Method S4 for more details.
The ratiometric threshold of 1.5-to-1 or greater was set as the ratiometric threshold criteria for probe positivity (i.e., 1.5-to-1 ratiometric threshold criteria method).
More suggestions(15)
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