[BioC] RG.MA in limma

Wang, Jixin jixinwang at tamu.edu
Mon Mar 9 06:58:28 CET 2009

Dear All,
I have one question that has perplexed me for a while. I use two color arrays and I want to get the normalized log2 intensity values instead of M values in MA$M (say, I have four arrays and I want to get eight channels (red and green) of normalized expression data. How can I get them?  I have checked the RG.MA function in R and have confused about this problem. I always got error messages whenever I try. Any help will be greatly appreciated!

In R help for package limma, it said 
MA.RG converts an unlogged RGList object into an MAList object. MA.RG(object) is equivalent to normalizeWithinArrays(object,method="none"). 
RG.MA(object) converts back from an MAList object to a RGList object with unlogged intensities.

>  RG.MA$R <- 2^(MA$A + MA$M/2)
Error in RG.MA$R <- 2^(MA$A + MA$M/2) : 
  object of type 'closure' is not subsettable
> RG.MA$G <- 2^(MA$A - MA$M/2)
Error in RG.MA$G <- 2^(MA$A - MA$M/2) : 
  object of type 'closure' is not subsettable

R version 2.8.1 (2008-12-22) 
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] limma_2.16.4

Best Regards,


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