Normalization of array-CGH data: influence of copy number imbalances

BMC Genomics

Table 3 Effect of pre-normalization to correct spatial bias prior to applying popLowess

	un-normalized*	popLowess**	pre-normalization by block-based Median***	pre-normalization by block-based Lowess****
XY vs XY	0.062	0.062	0.009	0.003
XY vs XY	0.067	0.067	0.003	0.003
XX vs XX	0.097	0.069	0.035	0.003
XX vs XX	0.125	0.127	0.031	0.004
XXX vs XX	0.051	0.049	0.003	0.004
XX vs XY	0.046	0.045	0.003	0.003
XXXX vs XX	0.060	0.033	0.004	0.004
XXX vs XY	0.058	0.058	0.007	0.005
XXXX vs XY	0.060	0.058	0.008	0.004

Standard deviation of medians of M from pin-tip blocks. Standard deviation is calculated before normalization* and after normalization using popLowess alone** or together with a pre-normalization step. Applied pre-normalization steps include either block-based Median*** or block-based Lowess****.

ISSN: 1471-2164