How to normalize 2 samples having 6 separate treatments


I have 2 samples, for which I have 6 different treatment conditions.

Should I be normalizing this data? Given that it's only 2 separate samples, but overall 12 (6*2), I'm not sure if I should. And if I do, should I perform it on all 12 samples together, or for each condition separately (i.e. 6 times separately for each of the two samples per each condition)?

I usually use RLE normalization (this is RNA-seq data).



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