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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