Table 2.

Disparities of the technical approaches

SAGE

• Sequence errors (although it has been shown that most of the single-copy SAGE tags are not generated from experimental sequence errors, but that they are novel tags derived from novel transcripts [53])

• Tag annotation difficulties

• Missing transcripts due to absence of a recognition site for the anchoring enzyme (approximately 0.7%) or GC-content bias [24,54]

• Incorrect tags arise from incomplete digestion or alternative poly-adenylation [55]

• Sequence polymorphisms resulting in multiple tags for a single transcript

Affymetrix HG-U133 GeneChips

• Probe design issues (such as distance of the target sequence from the poly-A tail; secondary structures within the target sequence; cross-reactivity of the probe with other transcripts, nucleic acid structure)

• Differences in hybridization efficiencies between probe sets

• Incorrect annotation of transcripts (no sequence verification)

• Efficiencies in dye incorporation