To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("normalize450K")

In most cases, you don't need to download the package archive at all.

normalize450K

Preprocessing of Illumina Infinium 450K data

Bioconductor version: Release (3.4)

Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.

Author: Jonathan Alexander Heiss

Maintainer: Jonathan Alexander Heiss <jonathan.heiss at posteo.de>

Citation (from within R, enter citation("normalize450K")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("normalize450K")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("normalize450K")

PDF	R Script	Normalization of 450K data
PDF		Reference Manual
Text		LICENSE

Details

biocViews	DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, Software, TwoChannel
Version	1.2.0
In Bioconductor since	BioC 3.3 (R-3.3) (1 year)
License	BSD_2_clause + file LICENSE
Depends	R (>= 3.3), Biobase, illuminaio, quadprog
Imports	utils
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Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	normalize450K_1.2.0.tar.gz
Windows Binary	normalize450K_1.2.0.zip
Mac OS X 10.9 (Mavericks)	normalize450K_1.2.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/normalize450K/tree/release-3.4
Package Short Url	http://bioconductor.org/packages/normalize450K/
Package Downloads Report	Download Stats

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