Statistics on the non-control, investigated and annotated probesets, together with the number of involved genes and proteins, are shown in Table 1 . It is evident that the proportion of genes covered by our annotated probesets to those covered by all non-control probesets ('gene retaining percentage' in Table 1 ), 95.2% for MOE430A_2 and 85.4% for HG-U133A, are higher than the corresponding probeset retaining percentages, 83.5% and 68.8%, indicating that the gene coverage has only been slightly reduced by our filtering procedures. This observation is in support of our primary goal, that is to refine gene-level probeset annotations to transcript-level, but not to simply remove the poor-quality gene-level annotations.