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Missing value imputation and outlier testing was performed by tailored in-house R scripts (Warth et al. 2015).
Our procedure involves parametric multivariate outlier testing using a multivariate Gaussian model, which we apply to principal components of the quality measure matrix.
Specifically, parametric outlier testing can be conducted on the basis of a fixed null mean and covariance for quality features derived from a family of arrays known to be of high quality.
ModuleSampleNetwork does not enable outlier testing and removal or data normalization, but instead seeks to compare module sample network properties between subgroups of samples (e.g. Figure 6) and across modules (e.g. Figure 4).
Based on the results of the outlier testing, three datasets were created consisting of: (i) all 60 loci, (ii) 59 loci, excluding the most severe outlier (Her14), and (iii) the most severe outlier, Her14, alone.
Similar(55)
Outliers are detected after running VIE_LSM/VIE_KALMAN by applying an outlier test (here, a simple 5- σ outlier test was used) or by manual inspection and are then removed in a second run already when reading in the data in VIE_INIT.
Assuming a normal distribution, Grubbs' outlier test can be used to remove one outlier.
We found one outlier among the control males group (Grubb's outlier test) and removed it from the analysis.
By using the Grubb's outlier test (significance level of α = 0.01), only one outlier was detected and, hence, discarded.
Outlier loci can be neutral or non-neutral and therefore relying solely on outlier tests to characterize the selection candidacy of loci risks a resulting high rate of false positives.
Let us define the outlier test function by (9).
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