In this paper, we linked the probesets of two widely used Affymetrix arrays with the International Protein Indexes (IPIs) [20, 21] through proper association and rigorous alignment procedures, and demonstrated the statistically significant advantage of interpreting microarray data at the transcript-level or protein-level. Our results can be viewed as a more precise annotation of Affymetrix array's probesets, with which one may achieve a more reliable interpretation of their experimental data. Moreover, the application of this new annotation substantially increased the expression correlation between interacting proteins.