Furthermore, we classified the probesets based on the way they linked to proteins. By checking the alignment results, the probesets in our annotation tables were divided into two groups, namely one-to-one and one-to-many. In our annotation table, a one-to-one probeset was linked to only a single protein, while a one-to-many probeset was linked to multiple proteins due to alternative splicing of one gene. The rest of the investigated probesets that were not linked to any protein were categorized into the third group of "one-to-null". The statistics of these three groups are shown in Table 2 . As we know, Affymetrix suffixes their probeset ID according to the probeset's specificity. The over ten types of probeset suffixes can be categorized into three groups: transcript-specific, with '_at', gene-specific, with '_a_at' or '_s_at', and other suboptimal probesets that may cross-hybridize with unrelated sequences. The first two groups are comparable to our one-to-one and one-to-many probesets respectively. However, we found that, out of a total of 21,097 and 16,213 investigated probesets in MOE430A_2 and HG-U133A respectively (Table 1) , our one-to-one type accounts for only 53.7% and 43.3%, which were significantly lower than that of _at probesets, 74.0% and 72.6%, in the respective arrays. This suggests that some of _at probesets are not really specific for a transcript.