\HeaderA{logitT}{logit-t and t-test by row}{logitT}
\aliasA{logitTStat}{logitT}{logitTStat}
\aliasA{logitTTransform}{logitT}{logitTTransform}
\aliasA{studenttTTest}{logitT}{studenttTTest}
\keyword{univar}{logitT}
\keyword{manip}{logitT}
\begin{Description}\relax
Functions for the logit-t test (Lemon et al. 2003) and the ordinary t-test computed for each row of an matrix.
\end{Description}
\begin{Usage}
\begin{verbatim}

logitTTransform(pm)
logitTStat(affy.batch,group)
studenttTTest(x, group)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pm}] A matrix of Pm intensities
\item[\code{affy.batch}] An AffyBatch object
\item[\code{group}] A group indicator vector, should have values 1 and 2 only.
\item[\code{x}] A matrix
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
See the definition (R-code) of each function for details.
\end{Details}
\begin{Value}
logitTTransform returns a matrix

logitTStat returns a vector with the logit-t statistic for each probe set.

studenttTTest returns a vector with t-statistic for each row of x.
\end{Value}
\begin{Author}\relax
Magnus \eqn{\mbox{\AA}}{}strand
\end{Author}
\begin{References}\relax
Lemon et al. (2003). A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol. 2003; 4(10):R67
\end{References}
\begin{Examples}
\begin{ExampleCode}
# ------------------------------------------
# Example analyzing the 6 arrays in the 
# AffySpikeU95Subset data set

# Loading the data
data(AffySpikeU95Subset)

# Vector with groups assignment 
group<-factor(rep(1:2,each=3))

# logit-T statistic
logitT<-logitTStat(AffySpikeU95Subset,
                   as.numeric(group))

# Computing RMA expression index
data.rma<-exprs(rma(AffySpikeU95Subset))

# Ordinary t-test by row/gene
studentT<-studenttTTest(data.rma, as.numeric(group))

# Comparing genes ranked top-20
logitTTop20  <- rank(-abs(logitT)) < 21
studentTTop20<- rank(-abs(studentT)) < 21
table(logitTTop20,studentTTop20)

\end{ExampleCode}
\end{Examples}

