\HeaderA{07.SingleChannel}{Individual Channel Analysis of Two-Color Microarrays}{07.SingleChannel}
\keyword{documentation}{07.SingleChannel}
\begin{Description}\relax
This page gives an overview of the LIMMA functions fit linear models to two-color microarray data in terms of the log-intensities rather than log-ratios.

The function \code{\LinkA{intraspotCorrelation}{intraspotCorrelation}} estimates the intra-spot correlation between the two channels.
The regression function \code{\LinkA{lmscFit}{lmscFit}} takes the correlation as an argument and fits linear models to the two-color data in terms of the individual log-intensities.
The output of \code{lmscFit} is an \code{MArrayLM} object just the same as from \code{lmFit}, so inference proceeds in the same way as for log-ratios once the linear model is fitted.
See \LinkA{06.LinearModels}{06.LinearModels}.

The function \code{\LinkA{targetsA2C}{targetsA2C}} converts two-color format target data frames to single channel format, i.e, converts from array-per-line to channel-per-line, to facilitate the formulation of the design matrix.
\end{Description}
\begin{Author}\relax
Gordon Smyth
\end{Author}