Dual-flashlight plot

In statistics, a dual-flashlight plot is a type of scatter-plot in which the standardized mean of a contrast variable (SMCV) is plotted against the mean of a contrast variable representing a comparison of interest .

[1] The commonly used dual-flashlight plot is for the difference between two groups in high-throughput experiments such as microarrays and high-throughput screening studies, in which we plot the SSMD versus average log fold-change on the y- and x-axes, respectively, for all genes or compounds (such as siRNAs or small molecules) investigated in an experiment.

[1] With the dual-flashlight plot, we can see how the genes or compounds are distributed into each category in effect sizes, as shown in the figure.

[3] The advantage of using SMCV over p-value (or q-value) is that, if there exist any non-zero true effects for a gene or compound, the estimated SMCV goes to its population value whereas the p-value (or q-value) for testing no mean difference (or zero contrast mean) goes to zero when the sample size increases .

[4] Hence, the value of SMCV is comparable whereas the value of p-value or q-value is not comparable in experiments with different sample size, especially when many investigated genes or compounds do not have exactly zero effects.