Improvements in replication for the TCGA-KIRC data set. (a) ROC curves for replication between a discovery and a validation data set. The validation data set was constructed to show in silico batch effects. (b) Concordance plots between an additional cohort assayed on the 27k array and the validation data set. Additional normalization methods are assessed in Additional file 1: Figure S4. Functional normalization shows a high degree of concordance between data sets. Funnorm, functional normalization; KIRC, kidney clear-cell carcinoma; ROC, receiver operating characteristic; TCGA, The Cancer Genome Atlas.