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All PCAs were performed with the free software package TMEV [ 75] with a default weighted covariance-estimation function.
A PCA was performed with the software package TMEv [ 91] for metabolite data using the default weighted covariance estimation function.
For the statistical analysis required for the metabolic profile analysis, PCA and two-way ANOVA were performed on the datasets obtained from metabolite profiling with the software package TMEV [ 64] using the default weighted covariance-estimation function.
The aim of the default Weighted Performance based HO Parameter Optimization algorithm (WPHPO) described in these articles is to dynamically modify the settings of the control parameters according to the current network performance situation, as opposed to them being set to fixed values at all times.
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Most contributors used the default weighting scheme for the method (e.g., SKAT) employed or else imposed a weighting scheme that effectively up-weighted rare variants.
Once the normalization factors for various damage categories have been computed, the respective damage factors are normalized according to them and then weighted using the default weighting factors of EI99.
Calculations were performed under the following conditions: deletions or insertions were double weighted; default setting of Epsilon (0) was chosen; transition/transversion ratio (TI/TV = 6.5).
Finally, the consistency with which participants rated how frequently they interrupted their prolonged sitting was assessed by percent agreement and a weighted kappa statistic (wκ) [ 35] with the default weights matrix in Stata 12.0.
SKAT's default weight resulted in low power (<40% at sample size of 450) because it severely down-weighted common variants, which contribute to a large proportion of disease risk in this dataset.
First, the annotation step was run with default evidence code weights, except that the evidence code IEA (Inferred from Electronic Annotation) was weighted 0. For the second round, unannotated sequences were passed through the annotation step using default evidence code weights.
The default SiteHopper PatchScore represents a summation of Tanimoto similarity coefficients [37] weighted 3 1 in favor of color similarity over shape similarity, yielding a continuous value between zero and four, conveying complete dissimilarity and perfect similarity respectively [13].
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