\HeaderA{contrastsFitM}{Compute Contrasts from Linear Model Fit}{contrastsFitM}
\keyword{methods}{contrastsFitM}
\begin{Description}\relax
Given a linear model fit to microarray data, compute estimated
coefficients and standard errors for a given set of contrasts. This
function was adapted from \code{\LinkA{contrasts.fit}{contrasts.fit}} of the
\emph{limma} package.
\end{Description}
\begin{Usage}
\begin{verbatim}
contrastsFitM(fit, contrasts)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fit}] an \code{\LinkA{MArrayLM}{MArrayLM}} object or a list
object produced by the function \code{\LinkA{lm.series}{lm.series}} or
equivalent.
\item[\code{contrasts}] numeric matrix with row corresponding to coefficients
in fit and columns containing contrasts. May be a vector if there is
only one contrast.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function was adapted from the equivalent
\code{\LinkA{contrasts.fit}{contrasts.fit}} limma's function to do the linear
model fit without use the empirical Bayes method given by the function
\code{\LinkA{eBayes}{eBayes}}.
\end{Details}
\begin{Value}
The result of this function is an object of class
\code{\LinkA{MArrayLM}{MArrayLM}}.
\end{Value}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>, adapted from
the limma's function.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{lmFit}{lmFit}}, \code{\LinkA{contrasts.fit}{contrasts.fit}},
\code{\LinkA{eBayes}{eBayes}}, \code{\LinkA{MArrayLM}{MArrayLM}}.
\end{SeeAlso}

