[BioC] Retrieving Adjusted Individual Channel Intensities

[Joseph Shaw [guest]]

Hi all,

Assume Cy5 (Channel 1) and Cy3 (Channel 2) dyes are used in a two-channel experiment; furthermore, assume background corrected intensities for both channels are passed through a loess normalization procedure using the limma package, resulting in data object MA as follows:

> MA <- normalizeWithinArrays(RGbk, method="loess")

Is there any way to achieve adjusted individual Cy3 and Cy5 intensity values (such that log2(Cy5/Cy3) = M.adj, where M. adj is a vector of the adjusted M values)?

Joseph

 -- output of sessionInfo(): 

No session info.

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