Using NEWS.Rd
oligoSnpSet, CopyNumberSet, and BeadStudioSet (defined in oligoClasses) require that all assayData elements are integer matrices. In particular, copy number should be scaled by 100 and coerced to integers and B allele frequencies should be scaled by 1000 and coerced to integers. The function integerMatrix(x, 100) in the oligoClasses package will coerce a matrix of doubles, 'x', to a matrix of integers scaled by a factor of 100. The hmm methods for these classes expect that the assay data elements are appropriately scaled integer matrices.