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*

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