histPvalue {a4Base} | R Documentation |
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.
histPvalue(object, ...) ## S4 method for signature 'limma' histPvalue(object, ...) ## S4 method for signature 'MArrayLM' histPvalue(object, coef, ...) ## S4 method for signature 'numeric' histPvalue(object, ...)
object |
either a numeric vector of p-values,
or an object of class |
... |
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 |
The histogram is displayed on the current device.
Willem Talloen and Tobias Verbeke
Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman \& Hall/CRC, p. 253.
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"]) }