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We analyzed data from NHAMCS, using the merged datasets from 2005 and 2006, with no exclusions.
For another, MiRNAClassify is compared with all the other methods simultaneously by using the merged datasets and our feature set.
Besides comparison with each method, respectively, we tested MiRNAClassify and other methods simultaneously by using the merged datasets about human, animal, and plant and the newly updated datasets and extracting a set of same features.
The peak height versus peak rank of the 1,648 high-confidence Kaiso peaks is plotted in Figure 2A (dashed line), for comparison with all peaks identified using the merged datasets (solid line).
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The corrected Brier score and AUC were improved slightly using the merged dataset.
To circumvent this problem, we also analyzed the condition-specific datasets separately (see Additional file 1 Fig. 1, 2, and 3) and obtained observations similar to those using the merged dataset.
Because IDR uses the merged dataset to call a final peak set, large peaks that are present in only one dataset may be included whereas certain small, but reproducible, peaks may be excluded.
Similar results were obtained using the merged breast cancer dataset (Additional file 6: Figure S3).
The total repeat base pairs were calculated for each sub-region using the merged partitioned repeats.
Anisotropic scaling was then applied to the merged datasets using Xprep (Sheldrick, 2008) to compensate both the anisotropy and scaling problems derived from radiation damage and the low symmetry space group.
For unsupervised cluster analysis, the average linkage hierarchical clustering algorithm was then applied to the merged datasets by using XCluster [ 39] with the centered correlation coefficient as the similarity/dissimilarity metric.
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