As a matter of fact, Affymetrix suffixes their probeset ID according to the probeset's specificity. For example, probesets that recognize unique transcript variants are suffixed with _at, and probesets that recognize multiple alternative transcripts from a single gene are suffixed with _a_at or _s_at, and so on. This suffix system gives a hint on the varied specificities of the probesets, and could be considered as an endeavor trying to do away with customers' worry about the gene-level data analysis strategy. However, the correctness of the suffix system has been in doubt [14, 18] . Therefore it is not reliable to perform transcriptlevel analysis on the basis of this imperfect suffix system. As the standard annotation files and most of the analysis algorithms are gene-oriented, analysts often average out the expression heterogeneity of the same gene when dealing with probeset level data [19] .