\Header{MArrayLM-class}{Microarray Linear Model Fit - class}
\keyword{classes}{MArrayLM-class}
\keyword{regression}{MArrayLM-class}
\begin{Description}\relax
A list-based class for storing the results of fitting gene-wise linear models to a batch of microarrays.
Objects are normally created by \code{\Link{lmFit}}.
\end{Description}
\begin{Section}{Slots/Components}
\code{MArrayLM} objects do not contain any slots (apart from \code{.Data}) but they should contain the following list components:
\describe{
\item[\code{coefficients}:] \code{matrix} containing fitted coefficients or contrasts
\item[\code{stdev.unscaled}:] \code{matrix} containing unscaled standard deviations of the coefficients or contrasts
\item[\code{sigma}:] \code{numeric} vector containing residual variances for each gene
\item[\code{df.residual}:] \code{numeric} vector containing residual degrees of freedom for each gene
}
Object may also contain the following optional components:
\describe{
\item[\code{genes}:] \code{data.frame} containing gene names and annotation
\item[\code{design}:] design \code{matrix} of full column rank
\item[\code{contrasts}:] \code{matrix} defining contrasts of coefficients for which results are desired
\item[\code{s2.prior}:] \code{numeric} value giving empirical Bayes estimated prior value for residual variances
\item[\code{df.prior}:] \code{numeric} vector giving empirical Bayes estimated degrees of freedom associated with \code{s2.prior} for each gene
\item[\code{s2.post}:] \code{numeric} vector giving posterior residual variances
\item[\code{t}:] \code{matrix} containing empirical Bayes t-statistics
\item[\code{var.prior}:] \code{numeric} vector giving empirical Bayes estimated variance for each true coefficient
}\end{Section}
\begin{Section}{Methods}
\code{RGList} objects will return dimensions and hence functions such as \code{\Link{dim}}, \code{\Link{nrow}} and \code{\Link{ncol}} are defined. 
\code{MArrayLM} objects inherit a \code{show} method from the virtual class \code{LargeDataObject}.

The functions \code{\Link{ebayes}} and \code{\Link{classifyTests}} accept \code{MArrayLM} objects as arguments.\end{Section}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\link{2.Classes} gives an overview of all the classes defined by this package.
\end{SeeAlso}

