The function intraspotCorrelation estimates the intra-spot correlation between the two channels.
The regression function 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 lmscFit is an MArrayLM object just the same as from lmFit, so inference proceeds in the same way as for log-ratios once the linear model is fitted.
See 06.LinearModels.
The function 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.