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This was followed by functional analysis on the data set level, and canonical pathway analysis.
All the procedures operate at a whole data set level.
Phylogenetic relationships among gastropod main lineages were inferred based on complete mt genome data both at the amino acid (13-protein data set) and nucleotide (allnuc data set) level using Lottia digitalis (Patellogastropoda), and Haliotis rubra (Vetigastropoda) as outgroups, respectively.
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Publicly available TCGA data sets (Level 2 and Level 3) were downloaded from NIH Bulk Downloadd' website (RNASeqV2: https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2).nci.nih.gov/display/TCGA/RNASeq+Version+2
To investigate the performance of the 80 sampling strategies, non-parametric bootstrapping was performed on 3-level hierarchical data sets, levels being subjects, days and measurements within days [ 29].
As shown in Table 4, the balanced accuracy of MetaVelvet-SL, even for the lowest similarity level of training data set (order-level training data set), was higher than MetaVelvet.
For all analysis performed for the data set, the level of significance was set as 0.05.
This was done for each crop data set, missing level and imputation method.
For multiple testing within one data set, the level of significance P<0.05 was adjusted according to the Bonferroni correction.
P values were determined by 10,000 Monte Carlo replications of the data set; a level of significance of 5% was adopted.
For the rat data set, the level of agreement between platforms in gene expression fold changes was dependent on the strain comparison (see Additional file 7).
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