X chromosome heterozygosity is a fairly sensitive heuristic to detect sample swaps, but not very specific. A variety of factors besides a crude sample mix-up will affect heterozygosity. Furthermore, if the goal is to enumerate as many samples with atypical sex karyotypes as possible, then X heterozygosity alone will not detect abnormalities such as triple X or XYY or homozygous X Kleinfelter syndrome. Examining the intensity of probe binding on the sex chromosomes will better resolve these cases. Illumina calls this intensity LogR ratio. On Affymetrix systems, it is simply known as probe intensity. These metrics, once suitably normalized, are roughly linear in copy number. Because there are tens of thousands of loci on the X chromosome on modern platforms, it is appropriate to examine a subsample of markers, and then take a measure of central tendency of each sample such as the median or mean intensity. The intensity plot provides a visualization of the intensity of X and Y probes (Figure 2). It is expected that females should have low Y intensity and high X intensity (bottom right corner),
