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. -- Sent via the guest posting facility at bioconductor.org.

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. Best, Jim 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. > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099