Data re-analysis. (A) There was a significant difference in the mean number of detected miRNAs (P < .0001, 1-way ANOVA), with significant individual differences between naive or éLTNP and MEU (P < .001, Bonferroni; NS indicates not significant). (B) Original/re-analysis differences using original exclusion criteria and normalization (first 3 rows) or stricter criteria (detected in > 80% of samples) and global normalization (bottom rows). No log₁₀ changes were reported for 114 miRNAs, and only 34 log₂ differences were seen. Naive versus éLTNP: the authors reported that miR-155 levels were significantly different, but in contrast with other studies, miR-155 was simply not detected in éLTNP or uninfected controls and was undetected or at low levels in naive. Bottom row: although Bignami et al provided values for some previously reported miRNAs,¹  the assertion of changes > 1 log₁₀ confuses interpretation. Re-analysis identified several previously reported miRNAs; miR-150 also appeared to be downmodulated in naive, but its abundance complicated interpretation of the quantile normalized data. Additional analyses (not shown) suggested differential expression of miR-150. (C) Across samples, U6 Cts varied from 11.9 (blue) to 15.8 (red), suggesting sample quality differences with implications for normalization choice. (D) Re-analysis using quantile normalized data. miRNAs differentially expressed in naive and éLTNP were used to cluster all samples (Pearson correlation, average linkage; patient numbers are at top and groups are color coded; for mean-centered data, blue represents greater abundance and yellow indicates low abundance/high Ct). Note that 3 naive samples (black underscore) diverge in expression of underexpressed miRNAs; disclosure of standard clinical parameters might reveal correlates of these differences.