Additional file 9: Figure S7.
Comparison between two methods for identifying differentially translated genes (DTGs), the false discovery rate (FDR)-validated method, and the ad hoc method. The figure shows all 18,757 genes that pass the ad hoc filter. Of these, the limma/FDR method with a twofold cut-off identified the genes marked in red and blue. When used with a twofold cut-off criterion, both methods identify very similar sets of mRNAs, but the ad hoc method also identifies those labeled green and orange. In contrast, when used with a 1.5-fold cut-off criterion (stippled lines), the ad hoc method yields a large number of additional genes, lying above and below the stippled lines, that have modest standard deviations (<0.5) but that are not selected by the limma/FDR method unless one relaxes the false-discovery criterion from 0.05 to as far as 0.4. s, significant by limma with an FDR threshold of <0.05; ns, FDR >0.05.
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Tiruneh et al. BMC Biology 2013 11:123 doi:10.1186/1741-7007-11-123