a4Base (version 1.16.0)

histPvalue: Plot the Distribution of P Values

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,  ...)
"histPvalue"(object, coef, ...)

Arguments

object

either a numeric vector of p-values, or an object of class tTest, limma or MArrayLM

coef

index of the coefficient for which the p values should be plotted; only applies to the MArrayLM method

...

further arguments passed to the method

Value

The histogram is displayed on the current device.

References

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

See Also

hist, histpvalueplotter

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"])  
}