GeneCount estimations with unknown tumor cell fraction. DNA copy number calculated by GeneCount, using a q-value within the range 0.7-0.9, a DI determined by flow cytomery, and the tumor cell fraction estimated by GeneCount in Figure 3, is plotted against the corresponding FISH result for 9 genes in (a) 55 and (b) 43 lymphomas. The smoothed array CGH ratio derived from GLAD and CGH-explorer was used in (a) and (b), respectively. Grey and blue columns represent GeneCount results that were consistent and inconsistent with the FISH data, respectively, after rounding off the GeneCount value. Frequency distributions are shown for each copy number, containing 1, 19, 134, 56, 11, 5, 4, and 1 value at a FISH copy number of 0, 1, 2, 3, 4, 5, 6, and 8, respectively, based on GLAD. The corresponding numbers based on CGH Explorer were 1, 15, 98, 48, 7, 5, 4, and 1.