I am performing an Affymetrix microarray analysis and aiming to identify differentially expressed genes. I have a list of differentially expressed genes after my analysis, however, there are some probe sets which are mapping to a single gene. For example, probe sets 209201_x_at, 211919_s_at, and 217028_at are mapping to CXCR4 with 3 different expression values.

What is an appropriate method to select a specific probe set if I want to identify differentially expressed gene? Is averaging the expression values of the probe sets for a single gene works?

Many thanks!