Hi dear all,
I am using limma for two color Agilent Microarray  analysis.
I found that normalizeBetweenArrays does not perform Quantile normalization
directly to the M values.
For that reason i had to use the following command
MA_Quantile<- noralizeBetweenArrays(*MA$M*,method="quantile")
To normalize M values i had to give MA$M instead of MA alone.
I want to make sure whether this way it is  correct or not and why M values
are not normalized directly while it is mentioned in limma user guide that
quantile method normalize M values.

This question was raised earlier in Bioconductor list (
https://stat.ethz.ch/pipermail/bioconductor/2011-May/039618.html) but there
is no answer for that.

Thanks



-- 
Neeraj KumarMolecular Reproduction Development and Genetics
Prof. Kondaiah' Lab
Indian Institute of Science
Bangalore 560012
Mobile # +91-9986295625

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