Predicted and empirical values of when extrapolating the accuracy.

<p>Empirical values of (black dots) of the ten replicates with different k-fold scenarios using 4′000 individuals and of the 20-fold runs of the fifty replicates using 5′698 Holstein-Friesian animals in total. Expected values (grey lines) use the number of derived with a Maximum-Likelihood approach in the original equation of Daetwyler et al. (2010) (D1, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081046#pone-0081046-g007" target="_blank">Figure 7A</a>) and in the modified equation of Daetwyler et al. (2010) (D2, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081046#pone-0081046-g007" target="_blank">Figure 7B</a>).</p

Fitted values of the number of independent chromosome segments () and weighting factors (w) with the Maximum-Likelihood approach and the corresponding natural logarithm of the likelihoods for method D2 and different SNP sets when using the Brown Swiss data set.

<p>Fitted values of the number of independent chromosome segments () and weighting factors (w) with the Maximum-Likelihood approach and the corresponding natural logarithm of the likelihoods for method D2 and different SNP sets when using the Brown Swiss data set.</p

Empirical values and expected values of for somatic cell score in Holstein-Friesian data.

<p>Empirical values of and expected values using the number of derived with a Maximum-Likelihood approach for the Holstein-Friesian data set in the original equation of Daetwyler et al. (2010) (D1) as well as in a modified form (D2) and in the equation of Goddard et al. (2011) without (G1) and with (G2) the proposed correction factor, respectively, and with the factor b not further determined (G3). For the empirical values, the mean and the standard deviation over the 50 replicates in each k-fold scenario of the Holstein-Friesian data set are shown.</p

Fitted values of the number of independent chromosome segments () and weighting factors (w) with the Maximum-Likelihood approach and the corresponding natural logarithm of the likelihoods for different methods and different SNP sets when using the Holstein-Friesian data set.

1<p>D2 is a modified equation of Daetwyler et al. (2010) while G3 is based on Goddard et al. (2011) with the weighting factor not defined like in the original publication but like in D2.</p

Empirical values and expected values of for milk yield and somatic cell score in Brown-Swiss.

<p>Empirical values of and expected values using the number of for the Brown Swiss data set derived with a Maximum-Likelihood approach in the modified equation of Daetwyler et al. (2010) (D2). For the empirical values of milk yield and somatic cell score in the Brown Swiss data set, the mean and the standard deviation over the 50 replicates in each k-fold scenario are shown.</p

Fitted values of the number of independent chromosome segments () and weighting factors (w) with the Maximum-Likelihood approach and the corresponding natural logarithm of the likelihoods when using the Holstein-Friesian data set.

1<p>D1 uses the formula of Daetwyler et al. (2010) to calculate the expected values of accuracy, G1 and G2 are based on Goddard et al. (2011) without and with the proposed correction factor, respectively. D2 is a modified equation of Daetwyler et al. (2010) while G3 is based on Goddard et al. (2011) with the weighting factor not defined like in the original publication but like in D2.</p

Regression of weighting factor w on the reciprocal of the logarithm of the marker density in Holstein-Friesian.

<p>Regression of the weighting factor w on the reciprocal of the natural logarithm of the marker density for the traits milk yield and somatic cell score in the Holstein-Friesian data set. The marker density was defined as the number of markers used divided by the length of the used parts of the genome in Morgan. The dots mark the values derived with the Maximum likelihood approach using the modified equation of Daetwyler et al. (2010) (D2) to describe the expected value of accuracy and the empirical data sets.</p

Regression of weighting factor w on the reciprocal of the logarithm of the marker density in Brown-Swiss.

<p>Regression of the weighting factor w on the reciprocal of the natural logarithm of the marker density for the traits milk yield and somatic cell score in the Brown Swiss data set. The marker density was defined as the number of markers used divided by length of the used parts of the genome in Morgan. The dots mark the values derived with the Maximum likelihood approach using the modified equation of Daetwyler et(2010) (D2) to describe the expected value of accuracy and the empirical data sets.</p

chicken data

chicken dat

Empirical values and expected values of for milk yield in Holstein-Friesian data.

<p>Empirical values of and expected values using the number of derived with a Maximum-Likelihood approach for the Holstein-Friesian data set in the original equation of Daetwyler et al. (2010) (D1) as well as in a modified form (D2) and in the equation of Goddard et al. (2011) without (G1) and with (G2) the proposed correction factor, respectively, and with the factor b not further determined (G3). For the empirical values, the mean and the standard deviation over the 50 replicates in each k-fold scenario of the Holstein-Friesian data set are shown.</p