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Old 11-25-2014, 03:43 PM   #1
Dampor
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Location: UK

Join Date: Jun 2012
Posts: 14
Arrow Question for experts in normalization

Hi Guys

I have replicated RNA-seq samples from 6 populations at 2 different treatments (benign and heat stress) repeated at two separate times (year 1 and year 2).
I am looking for the best way to normalize the reads before testing differential gene expression (I will be using GLM)

Possibilities:
a. All the samples normalized together.
b. Normalize by year: two separate normalizations (year 1 samples separate from year 2 samples).
c. Normalize by treatment: two separate normalizations (benign samples separate from heat stress samples)

I have a vague idea about which one would work better and need some expert opinion.

Thanks!
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