You need to be much more specific in your question if you expect to receive quality answers. There could be many reasons why your experiment isn't giving you the results you expect but it would be a guessing game without knowing details. Please elaborate as much as you can. How are you measuring copy number (array cgh, snp array, q-pcr, sequencing, etc)? What method did you use to calculate the copy number? What are you measuring copy number of, a particular gene, a few genes or genome-wide? Do you have controls, and if so what are they? The more details the better.