I am using the DEP package to identify the differentially expressed proteins from my MS results. I have a naive question about the results table. When we get a ratio of -2, for example, for protein A in the contrast Cond1vsCond2. Does that mean that protein A is underexpressed in Cond2 when comparing to Cond1? Or is it the other way around?
Thank you a lot in advance for your help!