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\name{mt.sample.teststat}
\title{Permutation distribution of test statistics and raw (unadjusted) p-values}
\alias{mt.sample.teststat}
\alias{mt.sample.rawp}
\alias{mt.sample.label}
\usage{
mt.sample.teststat(V,classlabel,test="t",fixed.seed.sampling="y",B=10000,na=.mt.naNUM,nonpara="n")
mt.sample.rawp(V,classlabel,test="t",side="abs",fixed.seed.sampling="y",B=10000,na=.mt.naNUM,nonpara="n")
mt.sample.label(classlabel,test="t",fixed.seed.sampling="y",B=10000)
}
\description{
These functions provide tools to investigate the permutation distribution
of test statistics, raw (unadjusted) \eqn{p}-values, and class labels.
}
\arguments{
\item{V}{A numeric vector containing the data for one of the variables (genes).}
\item{classlabel}{
A vector of integers corresponding to observation (column)
class labels. For \eqn{k} classes, the labels must be integers
between 0 and \eqn{k-1}. For the \code{blockf} test option,
observations may be divided into
\eqn{n/k} blocks of \eqn{k} observations each. The observations are
ordered by block, and within each block, they are labeled using the
integers 0 to \eqn{k-1}.
}
\item{test}{A character string specifying the statistic to be
used to test the null hypothesis of no association between the
variables and the class labels.\cr
If \code{test="t"}, the tests are based on two-sample Welch t-statistics
(unequal variances). \cr
If \code{test="t.equalvar"}, the tests are based on two-sample
t-statistics with equal variance for the two samples. The
square of the t-statistic is equal to an F-statistic for \eqn{k=2}. \cr
If \code{test="wilcoxon"}, the tests are based on standardized rank sum Wilcoxon statistics.\cr
If \code{test="f"}, the tests are based on F-statistics.\cr
If \code{test="pairt"}, the tests are based on paired t-statistics. The
square of the paired t-statistic is equal to a block F-statistic for \eqn{k=2}. \cr
If \code{test="blockf"}, the tests are based on F-statistics which
adjust for block differences
(cf. two-way analysis of variance).
}
\item{side}{A character string specifying the type of rejection region.\cr
If \code{side="abs"}, two-tailed tests, the null hypothesis is rejected for large absolute values of the test statistic.\cr
If \code{side="upper"}, one-tailed tests, the null hypothesis is rejected for large values of the test statistic.\cr
If \code{side="lower"}, one-tailed tests, the null hypothesis is rejected for small values of the test statistic.
}
\item{fixed.seed.sampling}{If \code{fixed.seed.sampling="y"}, a
fixed seed sampling procedure is used, which may double the
computing time, but will not use extra memory to store the
permutations. If \code{fixed.seed.sampling="n"}, permutations will
be stored in memory. For the \code{blockf} test, the option \code{n} was not implemented as it requires too much memory.
}
\item{B}{The number of permutations. For a complete
enumeration, \code{B} should be 0 (zero) or any number not less than
the total number of permutations.
}
\item{na}{Code for missing values (the default is \code{.mt.naNUM=--93074815.62}).
Entries with missing values will be ignored in the computation,
i.e., test statistics will be based on a smaller sample size. This
feature has not yet fully implemented.
}
\item{nonpara}{If \code{nonpara}="y", nonparametric test statistics are computed based on ranked data. \cr
If \code{nonpara}="n", the original data are used.
}
}
\value{
For \code{\link{mt.sample.teststat}}, a vector containing \code{B} permutation test statistics. \cr \cr
For \code{\link{mt.sample.rawp}}, a vector containing \code{B} permutation unadjusted \eqn{p}-values. \cr\cr
For \code{\link{mt.sample.label}}, a matrix containing \code{B}
sets of permuted class labels. Each row corresponds to one permutation.
}
\examples{
# Gene expression data from Golub et al. (1999)
data(golub)
mt.sample.label(golub.cl,B=10)
permt<-mt.sample.teststat(golub[1,],golub.cl,B=1000)
qqnorm(permt)
qqline(permt)
permt<-mt.sample.teststat(golub[50,],golub.cl,B=1000)
qqnorm(permt)
qqline(permt)
permp<-mt.sample.rawp(golub[1,],golub.cl,B=1000)
hist(permp)
}
\author{Yongchao Ge, \email{yongchao.ge@mssm.edu}, \cr
Sandrine Dudoit, \url{http://www.stat.berkeley.edu/~sandrine}.}
\seealso{\code{\link{mt.maxT}}, \code{\link{mt.minP}}, \code{\link{golub}}.}
\keyword{manip}
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