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Fig. 5 | Genome Biology

Fig. 5

From: Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

Fig. 5

False discovery rate and true positive rate of DE tools using simulated data from the NGP nutlin datasets. The actual FDR and TPR (at various nominal FDR) of eight DE tools from joint simulation and DGE analysis of mRNA and lncRNA. These particular results are from simulations with 25% true DE genes among 10,000 genes (constituting approximately 35% lncRNAs and 65% mRNAs) for designs with replicates per group. The curves represent the trade-off between the actual FDR and TPR at different nominal FDR (ranging from 0 to 100%). The points on the curve indicate the actual FDR and TPR values at 5% nominal FDR threshold. In general, DE tools’ performance for gene expression data simulated from the NGP nutlin dataset is better (low FDR and high TPR) than the performance observed from the Zhang based simulation, which can be explained by the difference in the intra-group biological variability. In line with the first simulation, DE tools’ performance appeared to be relatively lower for lncRNAs than for mRNAs

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