Dear all As we know a median normalization shifts the center of the log-ratio distribution to zero but does not affect the spread. when i plot a density plot after median normalization, impact of median normalization on spread of data is observed. you can observe the density plot in R as follows library(limma) targets=readTargets("SwirlSample.txt") RG=read.maimages(targets$FileName, source="spot") MA=normalizeWithinArrays(RG,method="none") M1=MA$M plot(density(M1,bw=0.17),main="density plots",xlab="log ratios", ylab="density",col=1,lty=1,lwd=3) MA=normalizeWithinArrays(RG,method="median") M2=MA$M lines(density(M2,bw=0.17),col=8,lty=1,lwd=3) I will be appreciate if you could me any hint about this issue Thank you in advance Regards -- *S. Fazeli MSc Student of Chem. Eng. ferdowsi University mashhad Iran* [[alternative HTML version deleted]]

Dear S Fazeli, Median normalization does not affect the spread of the M-values within each array, but it does affect the spread of the M-values between arrays. The whole purpose of normalization is to make different arrays more alike. You would be better off displaying boxplots by array, as illustrated in the limma User's Guide for the Swirl data set. Best wishes Gordon > Date: Sat, 18 Jun 2011 08:54:33 +0430 > From: samane fazeli <samanefazeli at="" gmail.com=""> > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] median normalization in limma > Message-ID: <banlktinj3wyrayk4slrctnyx6rsd8+fgfa at="" mail.gmail.com=""> > Content-Type: text/plain > > Dear all > As we know a median normalization shifts the center of the log-ratio > distribution to zero but does not affect the spread. > when i plot a density plot after median normalization, impact of median > normalization on spread of data is observed. > you can observe the density plot in R as follows > > library(limma) > targets=readTargets("SwirlSample.txt") > RG=read.maimages(targets$FileName, source="spot") > > MA=normalizeWithinArrays(RG,method="none") > M1=MA$M > plot(density(M1,bw=0.17),main="density plots",xlab="log ratios", > ylab="density",col=1,lty=1,lwd=3) > MA=normalizeWithinArrays(RG,method="median") > M2=MA$M > lines(density(M2,bw=0.17),col=8,lty=1,lwd=3) > > I will be appreciate if you could me any hint about this issue > Thank you in advance > > Regards > > > -- > *S. Fazeli > MSc Student of Chem. Eng. > ferdowsi University > mashhad > Iran* ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}