Included EBSeq for downstream differential expression analysis

[rsem.git] / EBSeq / man / MedianNorm.Rd

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+\name{MedianNorm}
+\alias{MedianNorm}
+\title{
+Median Normalization
+}
+\description{
+The median normalization from Anders et. al.2010
+}
+\usage{
+MedianNorm(Data)
+}
+\arguments{
+
+  \item{Data}{
+The data matrix with transcripts in rows and lanes in columns.
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+The function will return a vector contains the normalization factor for each lane.
+% ...
+}
+\references{
+Simon Anders and Wolfgang Huber: Differential expression analysis for sequence count data
+Genome Biology (2010) 11:R106 (open access)
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+GeneGenerate=GeneSimu(DVDconstant=4, DVDqt1=NULL, DVDqt2=NULL, Conditions=rep(c(1,2),each=5), NumofSample=10, NumofGene=10000, DEGeneProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, Meanconstant=NULL, OnlyData="Y")
+GeneData=GeneGenerate$data
+
+Sizes=MedianNorm(GeneData)
+# Run EBSeq
+EBres=EBTest(Data=GeneData, NgVector=rep(1,10^4), Vect5End=rep(1,10^4), Vect3End=rep(1,10^4), Conditions=as.factor(rep(c(1,2),each=5)), sizeFactors=Sizes,maxround=5)
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line