Dual-flashlight plot: Difference between revisions

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|title= Assessing the size of gene or RNAi effects in multifactor high-throughput experiments

|journal=Pharmacogenomics |volume=11 |issue= 2|pages=199–213

|year=2010 |pmid= 20136359|doi=10.2217/PGS.09.136 |url=}}</ref> 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.<ref name="ZhangPharmacogenomics2010"/>

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"/>

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|journal= Nature Genetics |volume=29 |issue= 4|pages=389–95

|year=2001 |pmid= 11726925|doi= 10.1038/ng766 |s2cid= 16841881

|url=}}</ref>

.<ref name=Cui2003>{{cite journal |vauthors=Cui X, Churchill GA |title=Statistical tests for differential expression in cDNA microarray experiments

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

|year=2003 |pmid=12702200 |doi= 10.1186/gb-2003-4-4-210|url= |pmc=154570
|doi-access=free
}}</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= 2|pages=292–99

|year=2010 |pmid= |doi=10.1198/sbr.2009.0074 |s2cid= 119825625

|url=}}</ref> 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 (statistics)|volcano plot]].

==See also==