A similar comparison was conducted for HG-U133A array, involving another transcript-level annotation by Harbig et al. [14] . Across the whole 28 datasets, the annotation by Harbig et al. showed advantage over Affy-protein-level annotation, while our transcript-level annotation performed best (p < 0.05 for 18 datasets under Student's t-test, see Figure 1B and Additional file 2). As our work was done two years later than Harbig et al.'s, the updated mRNA sequences in the probe-mRNA alignment is one of factors contributing to the increased performance. The other contributing factor is different approach we used to identify the mapping of probes to mRNA targets. Harbig et al. performed a two-phase blast: first, blast probeset target sequences against mRNA sequence pool, and then blast probe sequences against the retrieved mRNA sequences. Efficient as it was, this two-phase-blast strategy reduced the alignment precision as compared to our direct probe-against-mRNA blast strategy. Moreover, Harbig et al. accepted the mRNA with the highest average probe matches as the target of a probeset, even if the highest value could be suboptimal.