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MOTIVATION A common difficulty in large-scale microarray studies is the presence of confounding factors, which may significantly skew estimates of statistical significance, cause unreliable feature selection and high false negative rates. To deal with these difficulties, an algorithmic framework known as Surrogate Variable Analysis (SVA) was recently(More)
The 27k Illumina Infinium Methylation Beadchip is a popular high-throughput technology that allows the methylation state of over 27,000 CpGs to be assayed. While feature selection and classification methods have been comprehensively explored in the context of gene expression data, relatively little is known as to how best to perform feature selection or(More)
Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes(More)
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