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Fig. 2 | Genome Biology

Fig. 2

From: A practical guide to methods controlling false discoveries in computational biology

Fig. 2

FDR control in in silico experiments and simulations. a Observed FDR (y-axis) for various α-level cutoffs (x-axis) in the yeast RNA-seq in silico resampling experiment with spiked-in differentially expressed genes (left panel) and the simulation of yeast RNA-seq counts using the polyester R/Bioconductor package [28]. b Observed FDR (y-axis) across simulation settings at α-level of 0.05. The left panel displays FDR for increasing numbers of hypothesis tests and the right panel displays FDR for increasing proportions of non-null hypotheses. Note that the LFDR method is displayed as a dotted line when the number of tests per bin falls below 200 (where the number of bins is fixed at 20), as fdrtools generates a warning in this case that the estimation may be unreliable

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