easyRNASeq (version 2.8.2)

edgeR additional methods: Extension for the edgeR package

Description

This method extends the edgeR package by offering the functionality to plot the effect of the normalization factor.

Usage

## S3 method for class 'DGEList,character,character':
plotNormalizationFactors(obj = DGEList(),
  cond1 = character(1), cond2 = character(1))

Arguments

obj

An object of class DGEList

cond1

A character string describing the first condition

cond2

A character string describing the second condition

Value

• none

Examples

## create the object
	dgeList <- DGEList(counts,group)
	## calculate the sie factors
	dgeList <- calcNormFactors(dgeList)
	## plot them
	apply(combn(rownames(dgeList$samples),2),
		2,
		function(co,obj){plotNormalizationFactors(obj,co[1],co[2])},dgeList)