If your transgenic plants have selectable marker gene, such as nptII (for kanamycin resistance), you can find out the 'segregation rate' of the transgenic seedlings on selection-medium plates to figure out the possible transgene copy numbers. For example, 3:1 (resistant: susceptible) ratio give you an idea of possible 1 copy of transgene. However, it becomes complicated when the copies of the transgene increase.