Sensitivity, specificity, total rejection, and estimated false discovery rate comparisons between the RBMs and the PM for normal distributed gene expression data.

<p>Blue: PM; Grey: SAM; Red: RBM test statistic based permutation method; Orange: RBM -value based permutation method; Green: RBM test statistic based bootstrap method; Purple: RBM -value based bootstrap method. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2a:</a> sample size <i>n</i> = 4 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2b:</a> sample size <i>n</i> = 6 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2c:</a> sample size <i>n</i> = 12 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2d:</a> sample size <i>n</i> = 24 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2e:</a> sample size <i>n</i> = 48 in each group.</p

Comparison of sensitivities for all six methods.

<p><i>π</i>₁: Proportion of differentially expressed genes.</p><p>TSBP: RBM Test statistic based permutation method.</p><p>TSBB: RBM Test statistic based bootstrap method.</p><p>PBP: RBM <i>p</i>-value based permutation method.</p><p>PBB: RBM <i>p</i>-value based bootstrap method.</p

Possible outcomes of testing <i>m</i> null hypotheses.

<p><i>m</i> is the total number of null hypotheses.</p

Sensitivity, specificity, total rejection, and estimated false discovery rate comparisons between the RBMs and the PM for lognormal distributed gene expression data.

<p>Blue: PM; Grey: SAM; Red: RBM test statistic based permutation method; Orange: RBM -value based permutation method; Green: RBM test statistic based bootstrap method; Purple: RBM -value based bootstrap method. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2a:</a> sample size <i>n</i> = 4 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2b:</a> sample size <i>n</i> = 6 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2c:</a> sample size <i>n</i> = 12 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2d:</a> sample size <i>n</i> = 24 in each group; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080099#pone-0080099-g002" target="_blank">Figure 2e:</a> sample size <i>n</i> = 48 in each group.</p

Histogram of percentage of methylation at 485,577 loci.

<p>Histogram of percentage of methylation at 485,577 loci.</p

Commonly used experimental design for two color micoarrays.

<p>Commonly used experimental design for two color micoarrays.</p

Comparison of estimated false discovery rates for all six methods.

<p><i>π</i>₁: Proportion of differentially expressed genes.</p><p>TSBP: RBM Test statistic based permutation method.</p><p>TSBB: RBM Test statistic based bootstrap method.</p><p>PBP: RBM <i>p</i>-value based permutation method.</p><p>PBB: RBM <i>p</i>-value based bootstrap method.</p