Table 1 Summary of similarities between SAGE and Affymetrix HG-U133GeneChips for the final dataset (= 1094)
From: Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
|  | 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 expresssion 1 | 57% | 81% | 0.222 | 78% | 572 |
High expresssion 1 | 69% | 81% | 0.578 | 90% | 226 |
Significant difference 2 | 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
with n = tag count; N = Library size and p = n/N (proportion)