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diff --git a/EBSeq/man/IsoSimuAt.Rd b/EBSeq/man/IsoSimuAt.Rd
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--- a/EBSeq/man/IsoSimuAt.Rd
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-\name{IsoSimuAt}
-\alias{IsoSimuAt}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Isoform level simulation with outliers
-}
-\description{
-Simulate isoform level expression data from a Negative Binomial assumption. (With outliers)
-}
-\usage{
-IsoSimuAt(DVDconstant = NULL, DVDqt1 = NULL, DVDqt2 = NULL, Conditions, NumofSample, NumofIso = NULL, DEIsoProp, Phiconstant = NULL, Phi.qt1 = NULL, Phi.qt2 = NULL, NormFactor = NULL, OnlyData = T)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{DVDconstant}{
-Whether want to use constant fold change value for all the DE genes.
-}
-  \item{DVDqt1, DVDqt2}{
-If DVDconstant is not specified, the user could use a range of empirical DVD's f
-rom Gould' data. The lower and upper bound ( quantile) could be specified.
-The suggested value is c(.96, .97). DVD for each gene will be randomly choosed within the range.
-}
-  \item{Conditions}{
-A vector of charecters to show each sample's condition.
-(Only the two-condition case is supported now)
-}
-  \item{NumofSample}{
-Number of samples the user want to generate.
-}
-  \item{NumofIso}{
-Input should be a vector with length 3. All values should be non-negative.
-The ith value represents how many isoforms the user want to generate for isoform group i. 
-}
-  \item{DEIsoProp}{
-The proportion of isoforms to be generated as DE. The value should be in [0, 1].
-Besides, the same proportion of isoforms will be generated as EE isoforms with outlier.
-The genes will be generated as EE at first, then the count of one of the samples
-(randomly selected) will be setted as its original counts multiplied by one of (4, 6, 8, 10).
-
-}
-  \item{Phiconstant}{
-Whether set the disperse parameter phi to be a constant. If this parameter is specified, the settings of Phi.qt1 and Phi.qt2 will be ignored.
-Input should be a vector with length 3. The ith value indicates the overdisperse parameter of isoform group i.
-}
-  \item{Phi.qt1, Phi.qt2}{
-If Phiconstant is not specified, the user could use a range of empirical phi's from each group of Gould' data. The lower and upper bound ( quantile) could be specified.
-The suggested value is c(.25, .75). phi for each gene will be randomly choosed w
-ithin the range.
-
-}
-  \item{NormFactor}{
-Wether set the mean of each isoform to be a constant.
-}
-  \item{OnlyData}{
-Wether the user only want the generated data matrix. If OnlyData = T, the function will return the simulated matrix
-and the name of the DE genes.
-Otherwise the funtion will run DESeq, EBSeq, edgeR, baySeq and BBSeq and provide the results of each method.
-Currently only OnlyData=T is supported
-}
-}
-\details{
-For each isoform, we assumed that the expression follows a Negative Binomial distribution with mean mu_gi and variance mu_gi * (1 + mu_gi * phi_gi).
-For DE genes, we assumed that in one condition the genes are with mean mu_gi * DVD.
-mu, phi and DVD could be specified by the parameter settings.
-
-}
-\value{
-\item{data}{
-A list of expression values will be generated. 
-Each list represents a group of isoforms.
-Group1: Ng1
-Group2: Ng2
-Group3: Ng3
-The rows refer to the isoforms and the columns are the samples. 
-The isoforms are named "I_GroupNumber_IsoformNumber". The first part of the isoforms of each group will be the DE ones. (The number depends on the DEIsoProp parameter.)
-}
-\item{TrueDE}{The names of the isoforms who are defined to be DE.}
-
-\item{Outliers}{The names of the genes who are defined to be outliers at each level of (4,6,8,10).}
-}
-
-\references{
-%% ~put references to the literature/web site here ~
-}
-\author{
-Ning Leng
-}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-GeneSimu, IsoSimu
-}
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==>  Define data, use random,
-##--	or do  help(data=index)  for the standard data sets.
-IsoGenerate=IsoSimuAt(DVDconstant=NULL, DVDqt1=.97, DVDqt2=.98, Conditions=as.factor(rep(c(1,2),each=5)), NumofSample=10, NumofIso=NULL, DEIsoProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, OnlyData=T )
-
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line