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.

1 2 3 | ```
histPvalue(object, ...)
## S4 method for signature 'MArrayLM'
histPvalue(object, coef, ...)
``` |

`object` |
either a numeric vector of p-values,
or an object of class |

`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 |

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.

1 2 3 4 5 6 7 8 9 | ```
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"])
}
``` |

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