I am currently analyzing proteomics data as part of my master's thesis but I am struggling with the log transformation. I need to analyze iTRAQ LCMS data but I do not have the original data that came out of Proteome Discoverer. I need to start from the iTRAQ ratios (so intensity of the protein in a sample/intensity of the internal standard). The final goal is to have the fold change expression ratios of the patients compared to controls.
My question to you is: at which point do I perform a log2 transformation? I have 2 options:
- log2 transform the iTRAQ ratios --> calculate the mean abundance ratios per experimental group --> subtract the mean abundance ratios of patients with that of controls to obtain the fold change expression ratio
- calculate the mean abundance ratios per experimental group --> divide the mean abundance ratio of the patients by that of controls --> log2 transform this ratio
Which option is best and why?