\name{edgeR methods}

\alias{plotNormalizationFactors}
\alias{plotNormalizationFactors,DGEList,character,character-method}

\title{ 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{
	plotNormalizationFactors(obj=DGEList(),cond1=character(1),cond2=character(1))
}

\arguments{
  \item{obj}{An object of class \code{\linkS4class{DGEList}}}
  \item{cond1}{A character string describing the first condition}
  \item{cond2}{A character string describing the second condition}
}

\value{
	none
}

\examples{
	\dontrun{
	## 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)
	}
}

\author{Nicolas Delhomme}

\keyword{methods}