Figure 10
From: A comparison of probe-level and probeset models for small-sample gene expression data
Significance plots of NFM permutation results. (a-c) Histograms of NFM permutation p-values for the full data comparisons in each of the three spike-in datasets. (d-e) Bubble plots for the spike-in genes of the HGU95A and HGU133A spike-in datasets. The horizontal and vertical axes are the spike-in concentrations for the control and treatment conditions, with axis tick marks on the log scale. The size of the plotting character for each spike-in gene is proportional to the corresponding q-value (converted from NFM permutation p-values). Q-values less than 0.1 are represented as closed blue dots, while q-values greater than 0.1 are represented as open circles. Statistical significance (q-value < 0.1) is more common for genes with higher control and treatment concentrations. (f) The distribution of calculated NFM q-values (converted from NFM permutation p-values) by spiked-in fold-change for the spike-in genes of the Golden Spike dataset.