Correlated weak signal regions in Illumina Infinium array data. Signal intensity data from Illumina genotyping arrays (expressed as copy number counts per SNP), are shown in red above four example chromosome ideograms for two independently processed DNAs (S1 and S2), the data for which failed standard quality control checks. Whereas most markers can be seen to have produced normal strength signals (inferred diploid copy number of 2, indicated by the most prominent horizontal row of data points), many other markers produced far weaker signals (inferred copy number of one, indicated by the row of data points plotted one step lower), and these weak signal regions are highly correlated between the two samples (and between many others not shown here).
Veal et al. BMC Genomics 2012 13:455 doi:10.1186/1471-2164-13-455