Dear aroma users/authors, i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF values (B-allele frequency) as they were output from Illumina software. BAF is a normalized metric which reflects the proportion of B-alleles in each SNP, e.g. 0 for AA SNP, 0.5 for an AB SNP and 1 for BB. I have generated fracB values with aroma package and see now that there are also negative values for fracB, but as i understand it correctly BAF values should be in the range between 0 and 1. The question is, how can i convert fracB values into BAF values. Thank you in Advance.
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