All other data sets also had π values of 0.0006, except data set 7, for which π = 0.0008 (Fig. 3, Table S2).
We filtered our initial list of all candidate miRNA loci (miRDeep2 score with signal-to-noise ratio ≥10 (except data set 6: signal-to-noise ratio = 9.4) against a database of other small noncoding RNAs, including rRNAs, tRNAs, snoRNAs, snRNAs, 21U-RNAs, sbRNAs, and repeats to exclude false positives.
For all model data sets except our F2 data set, which is sparsely genotyped, we therefore calculated locus-specific P-values first.
We used 10fold crossvalidation on these datasets except for the data set from Chea et al. [37], on which 5fold crossvalidation was used instead.
The CTD-based gene sets ranked higher than the next-gen TM-based gene sets for all gene expression data sets except the ZnSO4 data set.
On one hand, when an appropriate inflation parameter is chosen (I = 1.5 in this experiment), MCL has an accuracy similar to that of Qcut, except for the data set with the highest noises, indicating a superior performance of graph-based algorithms in general.
The samples for the experiments were normal mouse liver and spleen RNA, which were purchased from Clonetech (Catalog No. 64042-1 liver; Catalog No. 64044-1 splexceptxcept for the data set GNF generated by Su et al. [ 9] at the Genomics Institute of the Novatis Research Foundation.
The identical reconstruction, preprocessing, and analysis steps were used on every data set, except that motion correction was performed using various configurations from each software package.
A complete processing was applied to each data set, except for Eurasia, India and Mexico that were provided partially processed.
This implies that all the variables in the data set except pH, K+, ({text{NO}}_{3}^) are factors that discriminate one cluster from the other.
From Table 3, it can be clearly found that Co-MIML is significantly better than MIMLfast on most data set (except for Reuters) with five evaluation criteria at significance level 95%, while We/Sp-MIML is better than MIMLfast on most data sets, except for on MSRA-v2 and Reuters.
