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The individual-level and the population-level approaches may produce very different numbers as the first calculates the value of R0, whilst the second calculates the value of a threshold parameter.
The model optimizes the maximum likelihood value of a threshold, such that the nodes before the threshold are identified as species diversification events, while the branches beyond the threshold are clusters following coalescent processes.
Differentially expressed genes were identified by significance analysis of microarray using a fold-change of 2. False-discovery rate is estimated by analyzing permutations of the measurements and expresses the percentage of genes identified as significant by chance for a given value of a threshold parameter delta.
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Specifically, the number of expressed genes (Y axis), depending on the sequencing depth f (X axis), for different values of a threshold parameter is presented in Fig. 4.
26 We evaluated a linear threshold model repeatedly for a wide range of possible values of a threshold dose (d0), modelling the risk function ERR on doses d as β(d−d0) for d>d0 or d=0 for d≤d0.
Finally, EPI is a "smoothed" version of GPI, obtained by averaging a slightly modified form of GPI over all possible values of a threshold for statistically significant differential gene expressions.
This suppresses possible signal that falls between the value of a symmetric threshold and Ek in a given tumor.
In addition, the predictive value of a PPV threshold of 13% was also evaluated.
For low values of ΔT, a threshold can de defined depending on the R ratio.
Results were expressed in the number of cycles (Ct value) at a threshold of 100,000 ΔRn.
For binary (yes/no) classification, the output of the ANN was converted to binary value using a threshold value of θ = 0.5.
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