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Table 2 Disparities of the technical approaches

From: Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

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