Comparing the S:N ratio before and after wave correction. The S:N ratios for all clones/samples called as CNVs in  calculated before and after wave correction are plotted on the x- and y-axes, respectively. For a clone flagged as a CNV in a given sample, the S:N ratio is defined as its log2 ratio divided by the standard deviation of all log2 ratios on the chromosome on which the CNV is located (for that sample). The red line has a slope of 1 and intercept 0. Points plotted above this line show an increase in S:N ratio after wave correction.
Marioni et al. Genome Biology 2007 8:R228 doi:10.1186/gb-2007-8-10-r228