I've got protein MS data that contains 3 technical replicates. For all I know, technical replicates can examine the repeatability of technology. So, I will focus on those overlapped proteins between all 3 replicates. After that, I want to conduct differential expression analysis. Here comes the question. How do I do with the data from 3 replicates? Average 3 protein density values of 3 replicates as the protein's density? Is that OK? OR some other good ideas?
Any advice will be appreciated.
THX in advance.