histPvalue: Plot the Distribution of P Values

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

This function displays the distribution of the p values using a histogram; the horizontal line represents 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. This uniform distribution is used to estimate the proportion of differentially expressed genes.

Usage

histPvalue(object, ...)

## S4 method for signature 'limma'
histPvalue(object, ...)

## S4 method for signature 'MArrayLM'
histPvalue(object, coef, ...)

## S4 method for signature 'numeric'
histPvalue(object, ...)

Arguments

object	either a numeric vector of p-values, or an object of class tTest, limma or MArrayLM
...	further arguments passed to the method
coef	index of the coefficient for which the p values should be plotted; only applies to the MArrayLM method

Value

The histogram is displayed on the current device.

Author(s)

Willem Talloen and Tobias Verbeke

References

Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman \& Hall/CRC, p. 253.

Examples

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"])  
}

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.