[BioC] RG.MA in limma
Naomi Altman
naomi at stat.psu.edu
Mon Mar 9 21:47:53 CET 2009
The problem is that you have tried to create a list called RG.MA
without initializing it first. All you need to do is use the RG.MA
function - i.e.
RGnorm=RG.MA(MA)
takes the M and A components of your normalized data "MA" and writes
them back into an object called RGnorm along with any other
components of MA, such as the
annotation.
--Naomi
At 01:58 AM 3/9/2009, Wang, Jixin wrote:
>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
>
>sessionInfo()
>R version 2.8.1 (2008-12-22)
>i386-pc-mingw32
>locale:
>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,
>
>Wang
>
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Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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