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. 2013 Jul;19(7):876–888. doi: 10.1261/rna.035055.112

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© 2013; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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FIGURE 5. — Assessment of true down-regulated and false up-regulated miRNAs in Dicer1-deficient samples. Curves showing the number of differentially expressed miRNAs detected by the miRNA microarrays between days 2 and 4, at various FDR cutoffs, for each normalization technique applied (see Table 3). The analyses shown are restricted to 209 miRNAs that were validated as true down-regulated miRNAs by TaqMan RT-qPCR arrays, also present on the Affymetrix platform (see Materials and Methods). The number of miRNAs confirmed to be significantly “true down-regulated” (A) and significantly “false up-regulated” (B), using the qPCR data as a reference, are given. The arrows highlight the better performance of normexp + cyclic loess + RMA and robust normexp + cyclic loess + RMA with array weights, which gives the highest amount of true down-regulated miRNAs at the most stringent FDR cutoffs of 0.05 and 0.1 (A), while giving a minimum of false up-regulated miRNAs (B).