Dear all,

I have a single colour experiment with paired samples (samples before and after treatment from the same mouse) and different treatments. I read the section in the limma user guide dealing with paired samples, but am not convinced that this is the best approach for my case.

Would it be correct to simply subtract the expression values after-before for each mouse and then use limma on these subtracted values to estimate the effect of the treatment?

Many thanks in advance for your ideas!
Best
Klemens

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