[BioC] boxplot

[axel.klenk at actelion.com]

Dear Paz, 

not sure I understand your question completely but does

library("limma")
RGn <- RG.MA(MA)
boxplot(log2(RGn$R))
boxplot(log2(RGn$G))

do what you want?

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Paz Tapia Ramirez <pazveron at hotmail.com>
To:
<bioconductor at stat.math.ethz.ch>
Date:
20.08.2011 08:08
Subject:
[BioC] boxplot
Sent by:
bioconductor-bounces at r-project.org











Hello, I have a question to plot a normalized result, look what I've done 
is the following:


library(marray)
library("hgug4112a.db")
library(annotate)
my.filenames <- c( "1.txt",
                   "2.txt",
                   "3.txt",
                   "4.txt")

one.col<-list(    R="gMeanSignal",G="gProcessedSignal",
           Rb="gBGMedianSignal",Gb="gProcessedBackground")
RG <- read.maimages(my.filenames, source="agilent", columns=one.col, 
dec=".")

 RG <- backgroundCorrect(RG, method="half", offset=50)
 MA <- normalizeBetweenArrays(RG,method="quantile")


but I want to plot the normalized results with boxplot, but I don't that 
argument will be passed to the function boxplot
.

 Thanks


    
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