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For computing the most probable value of validation, we used the minor allele frequencies for the genotyped SNPs, as shown in Additional file 1: Figure S9.
These were genotyped in a cohort of 468 individuals of two ethnicities, providing validation for 184 of the variations, as compared to a most probable value of validation of 197 ± 2 based on the cohort size and specific minor allele frequencies (validation rate of 93.4%).
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In spite of presence of large number of compounds in the training and test sets (3:1 in size ratio), we did not omit any compounds showing outlier behavior to artificially show enhanced values of validation metrics thus ensuring the predictive quality of the models for diverse types of compounds.
Since 14 of the 23 genes are already known to be reactive to Insig1, these results represent a highly significant validation success of NEO; using the 23388 genes on the array and assuming that there are 200 known genes downstream of Insig1 (a conservative estimate), the Fisher exact p-value of validation success is p = 1.0 × 10-13.
For each endpoint, Matthew's correlation coefficient (MCC) of internal validation was improved using the MFS method, and values of validation dataset also performed well.
The presence of bias in GEBV was evaluated by regressing true (g) genotypic values of validation animals on their predicted genotypic values (Table 4).
Our study obtained elevated values of validation parameters and detected that 53.1% of BV-AA-positive samples included two or more BV-AAs simultaneously: 30.9% showed two simultaneous bacteria, 25.6% three, 12.8% four, 2.3% five, and 1.2% six.
The predictive values of validation data were obtained according to the corresponding LR equations by a threshold (for successful or unsuccessful decisions) with equal sensitivity and specificity for the training data.
The bootstrap value of the validation dataset was 0.768 955% CI: 0.763 0.774).
Even though this action would greatly improve the value of antibody validation, an additional source of antibody variability would remain, namely lot-to-lot variability.
The median OS value of the validation samples assigned to the first and fourth clusters were 464 and 3147 days, and that for the second and third clusters were not reached.
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