Table 5 Consistency analysis with and without background adjustment under slide-wised and block-wised normalization strategies (the cutoff p-value is 10-5)
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 | 1447(32.27)a(78.85)b | 1045(44.69) (70.62) | 467 |
| Â | TW-SLM | 2907(58.93)(39.25) | 2791(61.38)(26.44) | 1713 |
| Â | Common2 | 1141 | 738 | - |
Block-wised | LOWESS | 1551(37.91)(76.47) | 1464(40.16)(59.84) | 588 |
| Â | TW-SLM | 2545(48.84) (46.60) | 2267(54.83) (38.64) | 1243 |
| Â | Common2 | 1186 | 876 | - |
Without background subtraction | ||||
Slide-wised | LOWESS | 1240(37.98) (86.05) | 1599(29.46) (77.42) | 471 |
| Â | TW-SLM | 1924(72.77)(55.46) | 3237(43.25)(38.25) | 1400 |
| Â | Common2 | 1067 | 1238 | - |
Block-wised | LOWESS | 1357(46.13)(82.68) | 2099(29.82) (69.46) | 626 |
| Â | TW-SLM | 1904(59.51)(58.93) | 2872(39.45) (50.77) | 1133 |
| Â | Common2 | 1122 | 1458 | - |
- 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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