GeneCount calculations with known tumor cell fraction. DNA copy number calculated by GeneCount is plotted against the corresponding FISH result for 9 genes in 94 lymphomas. The smoothed aCGH ratios from (a) GLAD and (b) CGH-explorer, a q-value of 0.8, and a DI and tumor cell fraction determined by flow cytometry were inputs to GeneCount. Grey and blue columns represent GeneCount results that were consistent and inconsistent with the FISH data, respectively, after rounding off the GeneCount number to the nearest integer value. Frequency distributions are shown for each copy number, containing 1, 25, 246, 66, 15, 5, 4, and 1 value at a FISH copy number of 0, 1, 2, 3, 4, 5, 6, and 8, respectively.