[BioC] RG.MA in limma

[Wang, Jixin]

Hi Naomi,
Thanks for pointing out the problem and providing the hint. I appreciate your kind help!

Best Regards,

Wang

----- Original Message -----
From: "Naomi Altman" <naomi at stat.psu.edu>
To: "Jixin Wang" <jixinwang at tamu.edu>, bioconductor at stat.math.ethz.ch
Sent: Monday, March 9, 2009 3:47:53 PM GMT -06:00 US/Canada Central
Subject: Re: [BioC] RG.MA in limma

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