The residual LRR variance prior to and after adjustment for C + G and CpG content. The log probe intensity ratio (LRR) values for each SNP or CNV assay provides data on probe intensity relative to that of the estimated genotype-specific cluster location. We implemented a method similar to that described in Staaf et al .  to re-estimate LRR after a quantile-normalization, with an enhanced multiple linear regression model, incorporating within-chip signal re-scaling terms and a polynomial correction for GC and CpG waves. This scatterplot shows the pre-normalization LRR variance against the LRR variance post-normalization.
Veal et al. BMC Genomics 2012 13:455 doi:10.1186/1471-2164-13-455