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. Author manuscript; available in PMC: 2015 May 1.
Published in final edited form as: Leukemia. 2014 Apr 15;28(11):2229–2234. doi: 10.1038/leu.2014.140

Table 3. Permuting class labels to assess the power of predicting CR.

During the training of classifiers, the treatment response labels were permuted 1000 times to measure the statistical significance of prediction performance. P-values indicate the proportion of total 1000 permutations giving better prediction performance than the original analysis using real treatment response labels. Hence, higher p-value suggests lower confidence in prediction analysis results using gene expression data.

Real CR % Predicted CR:
Positive Predictive Value % (p-value
– 1000 permutations)
IFM I 32 (44/136) 25 (0.36)
IFM II 36 (24/67) 27 (0.11)
HOVON 27 (76/282) 45 (0.13)
Mulligan et al. 43 (73/162) 43 (0.49)

Predicted CR or Positive Predictive Value is derived from the test or validation dataset analysis using criteria giving the best possible overall model accuracy.