It has been well established that alternative splicing increases mRNA diversity, and over 60% of human genes are involved in this mechanism [12] . In addition, other RNA processing events, such as RNA editing, also account for the increased diversity at the mRNA level [13] . Since these events enable one gene to encode multiple proteins which might be functionally heterogeneous, we feel it necessary to separate transcript-level synonymous probesets from gene-level synonymous ones. The probesets that hybridize to more than one transcript variant of the same gene are referred to as gene-level synonymous probesets; while the ones that hybridize to a single variant are named as transcript-level synonymous probesets. It has been noticed that transcript-level synonymous probesets tend to have similar expression profiles, while gene-level synonymous probesets may have distinct expression profiles [14, 15] . In fact, individual reports demonstrated that the expression of transcript variants could be totally different [16, 17] . These phenomena indicate that the gene-level strategy of microarray data analysis is imprecise enough that one may overlook the expressional inconsistencies among gene-level synonymous probesets.