I have a three biological replicates of treatment and Control samples. I am using MaxQuant for the data analysis . Currently, LFQ intensity has been log2 transform and then normalized. Normalized LFQ values then averaged for the triplicate samples. Ratio has been derived for Treatment vs Control. Is it a right approach?

Or first we have to take ratio of treatment vs control before log2 tranformation. Which is the correct sequence?

Regards

Chhaya

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