We have developed an OB-HMM approach for detecting copy number variation from BeadArray™ data (for details see the Materials and Methods section). In the model, hidden states denote the (unknown) copy number at each SNP. The states are inferred using the BeadArray™ genotyping data which comprises two signals at each SNP: (1) Log R ratios which are a measure of the magnitude of the combined fluorescent intensity signals from both sets of probes and (2) B allele frequencies which represent the relative ratio of the fluorescent signals from one allelic probe to the other. Figure 1 shows the log R ratios and B allele frequencies for one individual across chromosome 6 which includes a deletion.
