CNAmet v.1.2 User Guide Copy number arrays (array CGH or SNP arrays) and expression microarrays form an essential part of integrative analysis of cancer where the amount of genomic DNA can be linked to the amount of transcription [7]. However, aberrant DNA methylation also affects tumors in ways undetectable by an integrative analysis of copy number aberrations and expression alone [3]. We have designed and implemented the CNAmet algorithm and software package that facilitates the integrative analysis of high-throughput copy number, expression and methylation data. The package is written and distributed in the R statistical language [8].