I have doubts on making my samples comparable with each other. I have 3 replicates for each 2 group (Test and Control). I want to look at how proteins change. For that, I firstly did median centralization for each column of my replicate. Then, I applied a statistical test to compare 2 different conditions in order to find out which proteins change statistically. Then, I divided test group proteins to control and take the log2 value. At the end, I draw the volcano plot. (Since I am not comparing the samples, but proteins, applying the centralization is not a problem I think).
Do you think that my method is true? I know that when centralizing the data, standard deviation between each protein level is not standardized to 1. But, in which cases should I use median standardization and in which cases should I use median centralization. I have encountered many researchers have no idea about the median standardization and applying median scaling (dividing each replicate of data to median values). I am not much familiar with the concept, and have a little doubt about in which data set should I use normalization or standardization. Thank you in advance.