hellow everyone!

I will be delighted if any one can help me with this! I am working on a
microarray dual channel data, and i need to do a inter array normalization.
I have tried with quantile normalization (available in limma package) method
but the result i am getting is not satisfactory as the boxes are not
appearing to be of the same sizes which according to the fact should be the
same. can you please give me a reason for this. and is there any better
normalization method available for dual channel experiment.

regards
-- 
Veerendra.

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