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We also used an extension of the above REG procedure, where a permutation-based p-value for the hypothesis of no association of a target marker is computed by adjusting for the effect of a conditioning marker.
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The allele number, allele frequencies and polymorphism information content (PIC) of each marker were computed using PowerMarker version 3.25 ([Liu and Muse 2005]).
Therefore, BI trees for this marker were computed with MrBayes v.3.0b4 [ 55] with a mixed substitution model and a Gamma distribution of substitution rates with 4 categories.
b Mean distance between markers is computed as the arithmetic mean of the map distances between adjacent markers shown in Figure 2. c Arithmetic mean of the mean distance between markers in each linkage group.
Both classification error and the number of discovered markers are computed.
However, we think the essential improvement of the new method is that the external markers are computed based on the contextual information.
Genetic distances between markers were computed using Kosambi mapping function.
For each marker pair, the physical distance between markers was computed on a chromosome basis.
The distances between all possible pairs of markers were computed by Euclidean distance.
The phosphorylated/total ratio of MFIs for the protein markers was computed.
Our approach differs from the previous approaches predominantly in terms of how subnetwork markers are computed.
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