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Empirical p values for the linkage peaks were obtained by performing 10,000 simulations using SOLAR.
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Under the null hypothesis of uniformity, the P value for the linkage was calculated using the nonparametric computation as described by Price et al. (2004).
We randomly permute g i 's expression and compute the nominal p-value for the linkage between the random expression and a locus in the list and retain the smallest p-value.
If the values used for the linkage between synthetic data sets have not been synthesized, we can expect perfectly accurate linkages.
The RMP values for the SSR linkage map [ 7] were the percentage from the genetic location (cM) of each locus along the total length (cM) of the corresponding linkage group.
Empirical P values for the CNV-weighted linkage score analyses were also derived by gene dropping from simulated multilocus genotypes in MERLIN, using the same marker allele frequencies of the founders as in the unweighted linkage analysis simulations.
Table 4 and Additional file 7: Figure S3 show the mean polymorphism information content (PIC) values for each linkage groups in the whole collection, the fodder, spring and winter oilseed rape types, as well as in the "++", "0+" and "00" winter oilseed rape subgroups.
We obtain for the 7 hierarchical clustering algorithms the same behaviours than previously observed [ 49]: ranging from high CPP values for single linkage to low CPP values for Ward.
Table 4 summarizes the backward and forward linkage multiplier values for the six regions across the sectors.
The LD (linkage disequilibrium) values for the four pairs of SNPs and the probable haplotypes with their frequencies (Table 7) have been calculated.
If the values used in the linkage have not been masked, then we can expect perfect linkage accuracy.
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