Fig. 4.

Discrete copy number states at a commonly polymorphic site after PCC. The selected region (chr7:143504894-143707170, hg18 build) consists of a CNV locus (encompassing 170 probes) with 40 nonpolymorphic flanking probes on each side (X axis). Upper: the log ratio values of 2,028 hybridizations (Y axis) for all probes in the extended region are shown, for which rows are sorted in descending order by segment median ratios within the CNV. Lower: histograms of segment median ratios corresponding to the panels directly above. Following local normalization (Left) and LLN (Middle), varying copy number states are only moderately evident. PCC (Right) resolves at least six distinct states at this locus.