Changes in version 1.18.0 USER VISIBLE CHANGES o Using NEWS.Rd o 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.