Table 1

Summary of similarities between SAGE and Affymetrix HG-U133GeneChips for the final dataset (= 1094)

UP/DOWN classification

Contingency table diagonal

Pearson Correlation coefficient3

0–3 fold between-ratio difference

N


All transcripts

63%

76%

0.453

78%

1094

Low expresssion1

57%

81%

0.222

78%

572

High expresssion1

69%

81%

0.578

90%

226

Significant difference2

86%

47%

0.636

70%

167


1. Based on the binomial sampling error of SAGE tags, tags counts below 5.7 and 7.7 (per 100,000) for the WT and Stratagene sample, respectively, are not significantly different from tag count 0. When a tag falls below these thresholds in both libraries it is included in the "Low expression" group (line 2); when a tag counts is above these thresholds in both libraries it is included in the "High expression" group (line 3). The thresholds were calculated as the 95% confidence interval of the tag proportion: CI95%) = n ± 1.96* with n = tag count; N = Library size and p = n/N (proportion)

2.Significant difference between the two SAGE libraries is defined as a significant P-value (α<0.05) according to the Z-test between two libraries [21].

3.All observed correlation coefficients are significant at P < 0.01

van Ruissen et al. BMC Genomics 2005 6:91   doi:10.1186/1471-2164-6-91

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