a4 (version 1.20.0)

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,  ...)
## S3 method for class 'MArrayLM':
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"])  
}