Estimating baseline Log R Ratio adjustments due to ploidy. OncoSNP Log R Ratio baseline adjustments (red) for cancer cell lines (a) HL60 (Chr10), (b) HT29 (Chr3) and (c) SW1417 (Chr8). HL60 has a near-diploid karyotype and OncoSNP has correctly identified that no Log R Ratio baseline adjustment is required. HT29 and SW1417 have complex polyploid karyotypes and transformation of the SNP data to a virtual diploid state needs to baseline ambiguity for the Log R Ratio. For example, in (b) and (c), regions of allelic balance with negative Log R Ratios are identified. OncoSNP correctly locates the true baseline level for the Log R Ratio. In (d) the estimated Log R Ratio baseline adjustment for the ten cancer cell lines analyzed is found to show a strong linear correlation to the modal chromosome number of each cell line. Baseline adjustments are standardized for comparison against the Log R Ratio level associated with copy number 3 as the SNP data were acquired from different versions of the Illumina SNP array.