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Figure 5 | Genome Biology

Figure 5

From: GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Figure 5

GeneCount estimations in the t(14;18) translocated region involving BCL2. BCL2 copy number estimated by GeneCount, using a q-value of 0.8 and a DI and tumor cell fraction determined by flow cytometry, is plotted against the corresponding FISH result in 94 lymphomas. The smoothed array CGH ratios derived from GLAD and CGH-explorer were used in the left and right panels, respectively. Grey and blue columns represent GeneCount calculations that were consistent and inconsistent with the FISH measurements, respectively, after rounding off the GeneCount value. (a) Uncorrected FISH data are plotted; (b) these data were corrected as described in [22]. Frequency distributions are shown for each copy number, containing 1, 38, 33, 13, 5, and 1 value for a red spot FISH copy number of 1, 2, 3, 4, 5, and 6. The corresponding number of measurements for the corrected FISH data of 1, 2, 3, 4, 5, and 6 were 1, 69, 14, 4, 2 and 1.

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