[BioC] Retrieving Adjusted Individual Channel Intensities

James W. MacDonald jmacdon at uw.edu
Wed Jan 8 15:20:31 CET 2014

Hi Joseph,

I believe you want to use RG.MA(), so

rg <- RG.MA(MA)

will give you an RGList where rg$R and rg$G are the unlogged Cy5 and 
Cy3 intensities.



On Tuesday, January 07, 2014 7:58:39 PM, Joseph Shaw [guest] wrote:
> 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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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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