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

BMC Genomics

Table 1 Comparison of popLowess enriched population assignment to karyotyping data for eight hyperdiploid cases [21]

Case	Gain (called/karyotype)*	Diploid (called/karyotype)**	Gain (fraction of karyotype called)***
1	0.97	1.05	0.99
2	0.87	1.09	1.00
3	1.00	1.00	0.85
4	1.14	0.88	0.85
5	0.89	1.21	0.99
6	0.97	1.08	1.00
7	0.95	1.11	0.80
8	1.09	0.76	0.63

Two populations corresponding to a normal diploid population and a population of copy number gain were created using steps 1–5 of the procedure in figure 5. The ratio of probes called as belonging to the gain population and probes determined as gain according to karyotype data is shown*. The equivalent ratio for the diploid population is also shown**. In addition, the fraction of probes called correctly as gain within regions determined as gain by karyotype data is displayed***.

ISSN: 1471-2164