Figure 2

Median and Lowess normalization of aCGH data. Data is from a normal female with the karyotype 46, XX and a cell line with 47, XXX. Data sets with mimicked fractions of probes with gain (5, 10, 15, 20, 25, 30, 35, or 40 percent) were constructed by randomly omitting varying number of probes for autosomes. Box-plots display M values after normalization for data sets with varying fraction of probes with gain. (a) M values for X-chromosome probes after median normalization. (b) M values for autosomal probes after median normalization. (c) Genome plot after median normalization for the data with 35 percent of probes with gain. (d) M values for X-chromosome probes after lowess normalization. (e) M values for autosomal probes after lowess normalization. (f) Genome plot after lowess normalization for the data with 35 percent of probes with gain.