propdegenescalculation: Estimation of proportion of differentially expressed genes
In a4Base: Automated Affymetrix Array Analysis Base Package

Description Usage Arguments Value Author(s) See Also Examples

Estimation of proportion of differentially expressed genes. This estimation is based on a histogram of the p-values. More specifically, based on the horizontal line representing a uniform distribution based on the p value distribution between 0.5 and 1. This represents the hypothetical p value distribution arising just by chance. All genes with small p-values above this line reflect the expected number of differentially expressed genes not by chance.

1	propdegenescalculation(pValue)

pValue

a vector of p-values

proportion of differential genes

Willem Talloen and Tobias Verbeke

histPvalue

if (require(ALL)){
	data(ALL, package = "ALL")
	ALL <- addGeneInfo(ALL)
	ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
	
	tTestResult <- tTest(ALL, "BTtype")
	histPvalue(tTestResult[,"p"], addLegend = TRUE)
	propDEgenesRes <- propDEgenes(tTestResult[,"p"])
}