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Moreover, Froh has low prediction error variance, especially when SNP density is high.
Each element of the proximity matrix takes the value 1 or 0. If two mRNAs, say a and b, belong to the same terminal node, then [a, b] = 1, else [a, b] = 0. Though the proximity matrix obtained using a regression tree has low prediction accuracy, the use of a collection of trees greatly improves the prediction accuracy [ 20].
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After removing transcripts that are not polyadenylated or that were had low prediction values, we were able to examine 559 predicted ncRNAs.
None of the predictors had low prediction error or low variance, with an average 50% mean prediction error by cross validation (Additional files 2 and 3).
Among the 19 genes, 11 genes have high prediction values (more than 0.5), and eight genes have low prediction values (less than 0.5).
The best model was chosen as that which minimized the AIC, had lowest prediction variance and the smallest number viable of knots for the natural spline.
Among the pure linkage models (SF, JF, ESF, and EJF) and across all traits, map densities, and selection p thresholds tested, EJF models had the greatest prediction abilities, whereas SF models always had lowest prediction ability (Table S1, Table S2, and Table S3).
By use of the weighted Euclidean distance (WED), the novel index obtained (equation 3) will account for the importance of a given parameter in the context of the values of the other parameters – e.g., an outlying value of a parameter to which the prediction has low sensitivity should count less than that of a parameter with high sensitivity.
In CS30 predictions, MutaCYP has low to moderate correlation with the other methods (r = 0.12-0.38).
When a pathway has low completeness or lacks sufficient annotations, the predictions would have large deviations.
Other samples tested using MDA v.1 also had low scoring predictions for Influenza A and Leek yellow stripe potyvirus (see Table 1), which we suspect were due to non-specific binding.
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