Hi there, I want to do a simple ebayes analysis to find differentially expressed proteins using limma. I have a datset with 2000+ rows with proteins and 20 columns of which 9 are contols and 11 are cases. How should I use the model.matrix command to make a correct model.matrix so I can perform the ebayes test?

Any help would be greatly appreciated.

There are many, many examples in the limma User's Guide. You should read (and understand) what is presented there. If you don't understand those materials, you should really consult with a local statistician who does.