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), and the males show have similar level of X and Y intensities (top left corner). also In our dataset of 17,000 individuals two individuals were observed with mislabeled sex and XX individuals with XXY. Structural chromosomal variation can be identified using intensity only probes to calculate loss of heterozygosity and abnormal copy numbers using B allele frequency and Log R Ratio plots (Figure 3). The B allele frequency plot is the amount of B allele observed in a probe that should concentrate at zero for zero copy, at 0.5 for one copy and at 1 for two copies. Log R ratio is the ratio of a particular sample overall all samples. It is expected to concentrate at zero; sometimes an upward or downward bump is observed meaning amplification or deletion, respectively. These two plots can be obtained using Illumina BeadStudio/GenomeStudio.
