A comparison study of short SAGE versus GeneChip and long SAGE was conducted to determine if data were interchangeable between the techniques. Although SAGE and Affymetrix chip expression levels showed a significant correlation using the set of genes for which there was reliable and unambiguous mapping from tag-to-gene identification, correlation coefficients were low (0.51 for the Spearman's correlation coefficient with p < 0.0001). A quantitative analysis comparing the use of 10-bp SAGE tags to 17-bp SAGE tags indicated that the short SAGE technology was more efficient at identifying differentially expressed tags. However, 4-7% of the 10-bp tags were redundancies that could have been resolved by long SAGE and 10-20% of the short SAGE tags had no obvious match to currently annotated human transcript sequences.
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