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 [[alternative HTML version deleted]]

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 [[alternative HTML version deleted]] _______________________________________________ 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 The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com