Dual-flashlight plot
Encyclopedia
In statistics, a dual-flashlight plot is a type of scatter-plot in which the standardized mean (SMCV) is plotted against the mean of a contrast variable representing a comparison of interest
. The commonly used dual-flashlight plot is for the difference between two groups in high-throughput experiments such as microarray
s 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 siRNA
s or small molecule
s) investigated in an experiment.
As a whole, the points in a dual-flashlight plot look like the beams of a flashlight with two heads, hence the name dual-flashlight plot.
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. Meanwhile, we can also see the average fold-change for each gene or compound. The dual-flashlight plot is similar to the volcano plot. In a volcano plot, the p-value
(or q-value), instead of SMCV or SSMD, is plotted against average fold-change
. 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
. Hence, the value of SMCV is comparable whereas the value of p-value
or q-value is incomparable in experiments with different sample size, especially when many investigated genes or compounds do not have exactly zero effects. The dual-flashlight plot bears the same advantage that the SMCV has, as compared to the volcano plot.
. The commonly used dual-flashlight plot is for the difference between two groups in high-throughput experiments such as microarray
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
s and high-throughput screening
High-throughput screening
High-throughput screening is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry. Using robotics, data processing and control software, liquid handling devices, and sensitive detectors, High-Throughput Screening allows a...
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 siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
s or small molecule
Small molecule
In the fields of pharmacology and biochemistry, a small molecule is a low molecular weight organic compound which is by definition not a polymer...
s) investigated in an experiment.
As a whole, the points in a dual-flashlight plot look like the beams of a flashlight with two heads, hence the name dual-flashlight plot.
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. Meanwhile, we can also see the average fold-change for each gene or compound. The dual-flashlight plot is similar to the volcano plot. In a volcano plot, the p-value
P-value
In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...
(or q-value), instead of SMCV or SSMD, is plotted against average fold-change
. The advantage of using SMCV over p-value
P-value
In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...
(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
P-value
In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...
(or q-value) for testing no mean difference (or zero contrast mean) goes to zero when the sample size increases
. Hence, the value of SMCV is comparable whereas the value of p-value
P-value
In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...
or q-value is incomparable in experiments with different sample size, especially when many investigated genes or compounds do not have exactly zero effects. The dual-flashlight plot bears the same advantage that the SMCV has, as compared to the volcano plot.
See also
- Effect sizeEffect sizeIn statistics, an effect size is a measure of the strength of the relationship between two variables in a statistical population, or a sample-based estimate of that quantity...
- SSMD
- SMCV
- Contrast variable
- ANOVA
- Volcano plot (statistics)Volcano plot (statistics)In statistics, a volcano plot is a type of scatter-plot that is used to quickly identify changes in large datasets composed of replicate data . It plots significance versus fold-change on the y- and x-axes, respectively...