pvalHistogram: Histogram of the p values

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

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

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

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

## End(Not run)

AgiMicroRna documentation built on Nov. 8, 2020, 5:25 p.m.