Is male chromosome X similar to heterozygous deletions in autosomes?
No. One may think that by replacing the signal intensity of a segment of autosome by intensity of male chrX, he/she can create an artificial heterozygous deletion in autosomes, which is not correct. Autosome and chrX have different signal intensity distributions. When building reference clustering files, Illumina used both males and females: as a result, the expected ZERO value of LRR in chrX corresponds to ~1.5 copy of chrX, not 2 copies! To further understand this, one can open BeadStudio and examine by eye the mean intensity of chrX from multiple female individuals. The mean is not ZERO, but higher than ZERO, indicating that female chrX is not even similar to 2-copy autosomes. For more deails and discussions, refer to Sup Figure 1 of the 2007 PennCNV paper in Genome Research.
