Hi! I am trying to normalize phosphoproteomics data before doing a differential expression analysis (calculate fold changes and p-values) using ROTS* for 2 cell lines (4 replicates for the first and 3 replicates for the second)
In the package they recommend to normalize the data before by using "standard normalization techniques", but I am not sure what standard techniques are.
I have a dataset with the first column being the "gene and the phosphorylation site" and then seven columns following with the abundance for both cell lines in seven columns total.
I would appreciate your guidance on this simple issue! Thank you!