[BioC] fraction or difference

[Yolande Tra]

Hi list members,

May I have your expert opinion on the following.
I am looking for protein differentially expressed due to treatment of
a certain disease. Protein counts were measured before and after
treatment was given. Some patients respond to the treatment
(responders) and got better and some patients did not respond to the
treatment (nonresponders). The goal is to find which protein is
responsible for the positive response, so really looking at group
factor.
I have used two quantities to describe the change of these proteins:
ratio (after/before) and difference (after-before). After computing
these quantities, I considered the design as two independent groups
(responders versus nonresponders).
I used rankproduct procedure to detect the proteins of interest. I
obtained different lists of protein differentially expressed which
means that using different quantities afftect the results.

My question is which quantity (fraction or difference) is more
sensitive to a change in this situation?

Thank you for any suggestion and any insight in this question,
Yolande