I am working with SNP array data and would like to know what I should expect to see when a genome has lost both alleles at a segment.
The issue is, data for SNP arrays is reported as the Log2 R Ratio (LRR) and the B allele fraction (BAF). The LRR is supposed to be Log2(cn/2) where cn is the number of copies at a given SNP. So if there are 2 copies (i.e., for a normal segment of the genome) the LRR should be around 0; if there is 1copy (loss of copy) it should be around -1. But what about when there are 0 copies? Theoretically the LRR should be -Inf. But what does data actually look like at that point? Does one just see really low (negative) numbers? And how low? -10? -15? What does the assay actually tell you when you have 0 copies?
Here's a link to some Illumina documentation including description of LRR and BAF: https://www.illumina.com/Documents/products/technotes/technote_cytoanalysis.pdf