Histogram of the p values

Description

Creates an histogram of the pvalues. For multiple contrats, creates an histogram for every t.test pvalue (separate) or a single histogram for the F.test pvalue (nestedF). A uniform histogram will indicate no differential expression in the data set, whereas a right skewed histogram, will indicate some significant differential expression

Usage

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pvalHistogram(fit2, DE, PVcut, DEmethod, MTestmethod, CM,verbose=FALSE)

Arguments

fit2

MArrayLM object

DE

TestResults object

PVcut

limit p value to declare significant features

DEmethod

method for decideTests, only 'separate' or 'nestedF' are implemented

MTestmethod

method for multiple test

CM

contrast matrix

verbose

logical, if TRUE prints out output

Author(s)

Pedro Lopez-Romero

See Also

An overview of miRNA differential expression analysis is given in basicLimma An example of how to get the 'TestResults' object is in getDecideTests

Examples

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## Not run: 
pvalHistogram(fit2,DE,PVcut=0.10,
     DEmethod="separate",MTestmethod="BH",CM)

## End(Not run)