In statistics, a dual-flashlight plot is a type of scatter-plot in which the standardized mean of a contrast variable (
SMCV
In statistics, the standardized mean of a contrast variable (SMCV or SMC), is a parameter assessing effect size. The SMCV is defined as mean divided by the standard deviation of a contrast variable.
The SMCV was first proposed for one-way ANOVA ...
) is plotted against the mean of a
contrast variable In statistics, particularly in analysis of variance and linear regression, a contrast is a linear combination of variables (parameters or statistics) whose coefficients add up to zero, allowing comparison of different treatments.
Definitions
Let ...
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
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silic ...
s and
high-throughput screening
High-throughput screening (HTS) is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology, materials science and chemistry. Using robotics, data processing/control software, liquid handlin ...
studies, in which we plot the
SSMD
In statistics, the strictly standardized mean difference (SSMD) is a measure of effect size. It is the mean divided by the standard deviation of a difference between two random values each from one of two groups. It was initially proposed for qu ...
versus average log fold-change on the ''y''- and ''x''-axes, respectively, for all genes or compounds (such as
siRNA
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating ...
s or
small molecule
Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are ...
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 Volcano plot may refer to:
* Sabatier principle - a concept in chemical catalysis that relates the optimal concentrations of catalysts and substrates
* Volcano plot (statistics) - a type of graph used to relate fold-change to p-value that is common ...
. In a
volcano plot Volcano plot may refer to:
* Sabatier principle - a concept in chemical catalysis that relates the optimal concentrations of catalysts and substrates
* Volcano plot (statistics) - a type of graph used to relate fold-change to p-value that is common ...
, the
p-value
In null-hypothesis significance testing, the ''p''-value is the probability of obtaining test results at least as extreme as the result actually observed, under the assumption that the null hypothesis is correct. A very small ''p''-value means ...
(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 not comparable 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 Volcano plot may refer to:
* Sabatier principle - a concept in chemical catalysis that relates the optimal concentrations of catalysts and substrates
* Volcano plot (statistics) - a type of graph used to relate fold-change to p-value that is common ...
.
See also
*
Effect size
In statistics, an effect size is a value measuring the strength of the relationship between two variables in a population, or a sample-based estimate of that quantity. It can refer to the value of a statistic calculated from a sample of data, the ...
*
SSMD
In statistics, the strictly standardized mean difference (SSMD) is a measure of effect size. It is the mean divided by the standard deviation of a difference between two random values each from one of two groups. It was initially proposed for qu ...
*
SMCV
In statistics, the standardized mean of a contrast variable (SMCV or SMC), is a parameter assessing effect size. The SMCV is defined as mean divided by the standard deviation of a contrast variable.
The SMCV was first proposed for one-way ANOVA ...
*
Contrast variable In statistics, particularly in analysis of variance and linear regression, a contrast is a linear combination of variables (parameters or statistics) whose coefficients add up to zero, allowing comparison of different treatments.
Definitions
Let ...
*
ANOVA
Analysis of variance (ANOVA) is a collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means. ANOVA was developed by the statistician ...
*
Volcano plot (statistics)
Further reading
* Zhang XHD (2011
"Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi Research, Cambridge University Press"
References
{{DEFAULTSORT:Dual-Flashlight Plot (Statistics)
Bioinformatics
Statistical charts and diagrams