Functional normalization of 450k methylation array data improves replication in large cancer studies
We propose an extension to quantile normalization that removes unwanted technical
variation using control probes. We adapt our algorithm, functional normalization, to the …
variation using control probes. We adapt our algorithm, functional normalization, to the …
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies
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 …
which account for tumor purity. These methods are an extension of our previously developed …
Meffil: efficient normalization and analysis of very large DNA methylation datasets
Motivation DNA methylation datasets are growing ever larger both in sample size and
genome coverage. Novel computational solutions are required to efficiently handle these …
genome coverage. Novel computational solutions are required to efficiently handle these …
Adjusting for batch effects in DNA methylation microarray data, a lesson learned
EM Price, WP Robinson - Frontiers in genetics, 2018 - frontiersin.org
It is well-known, but frequently overlooked, that low-and high-throughput molecular data may
contain batch effects, ie, systematic technical variation. Confounding of experimental …
contain batch effects, ie, systematic technical variation. Confounding of experimental …
Batch effect correction for genome-wide methylation data with Illumina Infinium platform
Background Genome-wide methylation profiling has led to more comprehensive insights
into gene regulation mechanisms and potential therapeutic targets. Illumina Human …
into gene regulation mechanisms and potential therapeutic targets. Illumina Human …
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
Abstract Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime
candidate technology for Epigenome-Wide Association Studies (EWAS). However, a …
candidate technology for Epigenome-Wide Association Studies (EWAS). However, a …
quantro: a data-driven approach to guide the choice of an appropriate normalization method
SC Hicks, RA Irizarry - Genome biology, 2015 - Springer
Normalization is an essential step in the analysis of high-throughput data. Multi-sample
global normalization methods, such as quantile normalization, have been successfully used …
global normalization methods, such as quantile normalization, have been successfully used …
DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
Methylation of DNA is known to be essential to development and dramatically altered in
cancers. The Illumina HumanMethylation450 BeadChip has been used extensively as a cost …
cancers. The Illumina HumanMethylation450 BeadChip has been used extensively as a cost …
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data
J Maksimovic, JA Gagnon-Bartsch… - Nucleic acids …, 2015 - academic.oup.com
Due to their relatively low-cost per sample and broad, gene-centric coverage of CpGs across
the human genome, Illumina's 450k arrays are widely used in large scale differential …
the human genome, Illumina's 450k arrays are widely used in large scale differential …
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
Background Systematic technical effects—also called batch effects—are a considerable
challenge when analyzing DNA methylation (DNAm) microarray data, because they can …
challenge when analyzing DNA methylation (DNAm) microarray data, because they can …