Differential expression and comparison with RT-qPCR results. (A) Heat map for the t-statistics obtained from the linear model for the treatment response of the expression values of each miRNA. The dendrogram is based on the Euclidean distance between the t-values obtained from the various preprocessing pipelines (described in Additional file 1: Table S1). (B) Scatter plot of the mRNA differential expressions obtained from the normalized data of the SCN vs. AQN preprocessing pipelines. The miRNAs selected for the RT-qPCR experiment are indicated in red. (C) Bar chart of the Spearman’s correlation coefficients between the differential expression of the selected miRNAs obtained by RT-qPCR and those obtained from the preprocessing pipelines. The error bars are the 2.5th–97.5th percentiles of the values obtained from a simple leave-one-out re-sampling approach. (D) Scatter plot of the differential expressions of the selected miRNAs obtained by RT-qPCR and those obtained from the SCN pipeline. The error bars show the 95% confidence intervals calculated as t0.975,6 × (SCN differential expression/SCN t-statistic) and the solid circles represent statistically significant -∆∆CT values (t-test p-value < 0.05). The horizontal axes of Panels B and D are identical, so that the points of the two plots can be matched.