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Microarray duplicates - (Mar/03/2009 )

Hi all
A very basic question indeed but i would to get it clarified.
i wish to do methylation array using cell line samples,but i want to do in duplicates.Now how do i go about it,

i) whether take just the dna of the same sample in 2 slides,
ii)take 2 different dna(extracted separately) samples,but of the same cell line in 2 slides.



doing either answers different questions.

With array experiements you need to know what you are asking before pouring money into it.

For option a, same DNA sample run twice you are testing the reproducibility of the microarray platform.

For option b you are testing the variability of DNA methylation in your cell line culture (as well as the variability in the platform but you won't be able to tease them apart).

so really you need to ask yourself, what are you wanting to find out?