Table 2 Summary of normalization methods. Each of the normalization methods in this table will be denoted by its number through out the text. For full description of methods refer to "Methods of bias removal" section in Results and Discussion and the "Normalization methods" section in Methods.
From: A stepwise framework for the normalization of array CGH data
Method no. | Normalization method | Description |
|---|---|---|
Background subtracted | ||
1 | No normalization | Raw ratios |
Global method | ||
2 | Global median Ratio | Ratios scaled by their median |
Intensity dependant methods | ||
3 | Intensity LOWESS, 10% span | Global Intensity LOWESS, span = 10% |
4 | Intensity LOWESS, 25% span | Global Intensity LOWESS, span = 25% |
5 | Intensity LOWESS, 40% span | Global Intensity LOWESS, span = 40% |
Spatial methods | ||
6 | Print tip mean Ratio | Ratios of each print-tip group scaled by the mean ratio of that group |
7 | Spatial | median of log2 ratios for the spots within a spatial neighbourhood window of size 11 rows by 11 columns centred on that spot |
8 | Spatial + Median Plate Ratio | Method 8 followed by plate normalization |
Combined intensity dependent and spatial methods | ||
9 | Print Tip Intensity LOWESS, span = 40% | LOWESS performed on the ratios from each print-tip group |
10 | Intensity LOWESS + Spatial | Stepwise Method 4 and 8 |
Three step normalization | ||
11 | Intensity LOWESS + Spatial + Median Plate Ratio | Stepwise Methods 4 and 9 |
12 | Spatial + Median Plate Ratio + intensity LOWESS | Stepwise Methods 9 and 4 |
Background not subtracted | ||
13 | No Normalization | See Method 1, but without background subtraction |
Global method | ||
14 | Global median Ratio | See Method 2, but without background subtraction |
Intensity dependant methods | ||
15 | Global Intensity LOWESS, span = 10% | See Method 4, but without background subtraction |
Spatial methods | ||
16 | Print tip Mean Ratio | See Method 3, but without background subtraction |
17 | Spatial | See Method 8, but without background subtraction |
Combined intensity dependent and spatial methods | ||
18 | Intensity LOWESS + Spatial | See Method 10, but without background subtraction |
Three step normalization | ||
19 | Intensity LOWESS + Spatial + Median Plate Ratio | See Method 11, but without background subtraction |