Dual-flashlight plot: Difference between revisions

Revision as of 15:55, 20 June 2012

Revision as of 20:12, 20 June 2012

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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.<ref name="ZhangPharmacogenomics2010"/>

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 (statistics)|volcano plot]]. In a [[volcano plot (statistics)|volcano plot]], the [[p-value]] (or [[Q value (nuclear science)|q-value]]{{clarify}}), instead of SMCV or SSMD, is plotted against average fold-change <ref name=Jin2001>{{cite journal |author=Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G

|title= The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster

|journal= Nature Genetics |volume=29 |issue= |pages=389–95

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|title=Statistical tests for differential expression in cDNA microarray experiments

|journal= Genome Biology |volume=4 |issue= 4|pages=210

|year=2003 |month= |pmid=1270220 |doi= |url=}}</ref> 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

.<ref name=ZhangSBR2010>{{cite journal |author=Zhang XHD

|title= Strictly standardized mean difference, standardized mean difference and classical t-test for the comparison of two groups

|journal= Statistics in Biopharmaceutical Research |volume=2 |issue= |pages=292–99

|year=2010 |month= |pmid= |doi=10.1198/sbr.2009.0074 |url=}}</ref> Hence, the value of SMCV is comparable whereas the value of [[p-value]] or [[q-value]] is incomparable 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 (statistics)|volcano plot]].

==See also==