Additional file 7: of HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

Ten-fold internal cross-validations to identify an optimal DNAme signature. Upper panel shows the total misclassification error (y-axis) as a function of the shrinkage threshold (x-axis) used. Lower panel shows the misclassification error for each phenotype (1 = low HOTAIR expression, 2 = high HOTAIR expression) as a function of the same shrinkage threshold. The optimal minimal classifier was found at a threshold of approximately 1.47, corresponding to a 67-CpG signature at an estimated false discovery rate (FDR) of approximately 0.17 (not shown). The FDR was estimated using a permutation scheme as implemented in the pamr R-package, and the relatively low FDR (only about 17 % of the 67 CpGs are expected to be false positives) demonstrates the presence of a genuine DNAme signal associated with HOTAIR expression. (PDF 13 kb