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Geographic distances between all samples were computed with Geographic Distance Matrix Generator version 1.2.3 [ 126].
The gene expression values of the exon array samples were computed with the aroma.affymetrix [ 25] package of Bioconductor [ 26] in R [ 27].
The relative mRNA levels for each of the OsRR genes in different RNA samples were computed with respect to the internal standard, UBQ5, to normalize for variance in the quality of RNA and the amount of input cDNA.
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The relative expression level of the gene of interest in the patient samples was computed with respect to the internal standard.
We also show the computational advantage of using the Equivalent Planes method; large systems with small failure probabilities which take over 17 h for Monte Carlo directional sampling were computed with the Equivalent Planes in less than one second.
Subsequent maxima of the likelihood function associated with bootstrapped samples were computed by means of local optimization algorithms (e.g., downhill simplex or quasi-Newton).
Sample skew and sample excess kurtosis of time courses were computed with the R package FinTS.
Circular variance, test of circular uniformity and sampling from von Mises distribution were computed with the R package CircStats.
In the first study comparing different volume of whole saliva one-way repeated measure ANOVAs were computed with sample volume (.10,.25,.50, and 1.0 ml) as a 4-level independent variable.
First, local diffusion parameters were computed with 5000 sample streamlines and 2 fiber directions per voxel (Behrens et al. 2007).
According to the distribution of the correlations, the significance of the correlation of each cell line with tumor samples was computed (P value < 0.05).
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