Although Affymetrix utilized the most complete information available at the time of array design, tremendous progress in genome sequencing and annotation in recent years renders existing probeset designs and target identifications suboptimal. In recent years, there have been continuous reports on systematic false expression signals of Affymetrix probesets [39] , spurious expression correlation caused by cross hybridization [18] , and expressional inconsistency among different microarray platforms or even different generations of one platform [40] [41] [42] [43] . A few research groups performed probe-against-mRNA blast similar to ours [22, 42, 44] , but mostly they centered around UniGene [45] and therefore improved the accuracy of annotation only at gene level. A major trend among these efforts was to redefine probesets so that probes matching the same molecular target were placed into custom probesets, as proposed by [19, 23, 39, 42] , but as the authors of [19] pointed out, 'these transcript-targeted probesets are not transcript-specific, as probesets targeting transcripts from the same gene may share many or even all probes'. Thus the probe re-organization strategy may be used to make distinction at the level of genes, but not at the level of transcripts or splice variants [18] . Besides, this strategy takes the probe-level intensity file (the CEL file) as a prerequisite, however only around half of the expression datasets deposited in public databases like GEO were found with CEL files.