Quantifying and Normalizing Methylation Levels in Illumina Arrays
نویسندگان
چکیده
منابع مشابه
shinyMethyl: interactive visualization of Illumina 450K methylation arrays
Up to now, more than 10,000 methylation samples from the state-of-the-art 450K microarray have been made available through The Cancer Genome Atlas portal [1] and the Gene Expression Omnibus (GEO) [2]. Large-scale comparison studies, for instance between cancers or tissues, become possible epigenome-widely. These large studies often require a substantial amount of time spent on preprocessing the...
متن کاملA statistical framework for Illumina DNA methylation arrays
MOTIVATION The Illumina BeadArray is a popular platform for profiling DNA methylation, an important epigenetic event associated with gene silencing and chromosomal instability. However, current approaches rely on an arbitrary detection P-value cutoff for excluding probes and samples from subsequent analysis as a quality control step, which results in missing observations and information loss. I...
متن کاملThe minfi User’s Guide Analyzing Illumina 450k Methylation Arrays
Each sample is measured on a single array, in two different color channels (red and green). Each array measures roughly 450,000 CpG positions. Each CpG is associated with two measurements: a methylated measurement and an “un”-methylated measurement. These two values can be measured in one of two ways: using a “Type I” design or a “Type II design”. CpGs measured using a Type I design are measure...
متن کاملshinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
We present shinyMethyl, a Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an interactive interface is launched. Reactive plots allow fast and intuitive quality control assessment of the samples. In addition, exploration of the phenotypic associations is poss...
متن کاملAgreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time
Epigenome-wide association studies (EWAS) have focused primarily on DNA methylation as a chemically stable and functional epigenetic modification. However, the stability and accuracy of the measurement of methylation in different tissues and extraction types is still being actively studied, and the longitudinal stability of DNA methylation in commonly studied peripheral tissues is of great inte...
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ژورنال
عنوان ژورنال: Journal of Biometrics & Biostatistics
سال: 2013
ISSN: 2155-6180
DOI: 10.4172/2155-6180.1000164