Table 6 Consistency analysis with and without background adjustment under slide-wised and block-wised normalization strategies (the cutoff p-value is 10-3)
From: A robust two-way semi-linear model for normalization of cDNA microarray data
Normalization Strategy | Normalization Method | Direct comparison | Indirect comparison | Common genes1 |
|---|---|---|---|---|
With background subtraction | ||||
Slide-wised | LOWESS | 2563(44.52)a(79.05)b | 2234(51.07)(73.23) | 1141 |
| Â | TW-SLM | 4330(68.45) (46.79) | 4055(73.09) (40.35) | 2964 |
| Â | Common2 | 2026 | 1636 | - |
Block-wised | LOWESS | 2731(49.40)(78.58) | 2700(49.96) (66.74) | 1349 |
| Â | TW-SLM | 4085(61.32)(52.53) | 3645(68.72) (49.44) | 2505 |
| Â | Common2 | 2146 | 1802 | - |
Without background subtraction | ||||
Slide-wised | LOWESS | 2440(52.50) (82.99) | 3024(42.36) (79.27) | 1281 |
| Â | TW-SLM | 3615(77.01)(56.02) | 4400(63.27) (54.48) | 2784 |
| Â | Common2 | 2025 | 2397 | - |
Block-wised | LOWESS | 2694(57.24) (79.62) | 3495(44.12)(74.91) | 1542 |
| Â | TW-SLM | 3530(67.39) (60.76) | 4190(56.79)(62.48) | 2379 |
| Â | Common2 | 2145 | 2618 | - |
- Common1: intersection between the direct and the indirect comparison given the same method.
- Common2: intersection between the LOWESS and the TW-SLM given the same comparison.
- a: consistency between the comparisons expressed as the percentage.
. - b: the percentage of Common2 for each method.
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