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We present a set of statistical methods for the analysis of DNA methylation microarray data, which account for tumor purity. These methods are an extension of our previously developed method for purity estimation; our updated method is flexible, efficient, and does not require data from reference samples or matched normal controls. We also present a method for incorporating purity information for differential methylation analysis. In addition, we propose a control-free differential methylation calling method when normal controls are not available. Extensive analyses of TCGA data demonstrate that our methods provide accurate results. All methods are implemented in InfiniumPurify.   Electronic supplementary material  The online version of this article (doi:10.1186/s13059-016-1143-5) contains supplementary material, which is available to authorized users.

Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies