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Last seen 10.5 years ago
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
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