normalize450K: Preprocessing of Illumina Infinium 450K data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("normalize450K")
AuthorJonathan Alexander Heiss
Bioconductor views DNAMethylation MethylationArray Microarray Normalization Preprocessing TwoChannel
Date of publicationNone
MaintainerJonathan Alexander Heiss <jonathan.heiss@posteo.de>
LicenseBSD_2_clause + file LICENSE
Version1.4.0

View on Bioconductor

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/estimateLC.R R/read_and_normalize450K.R
R/sysdata.rda
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/read_and_normalize450K.R
inst/doc/read_and_normalize450K.Rnw
inst/doc/read_and_normalize450K.pdf
man
man/estimateLC.Rd man/read_and_normalize450K.Rd
vignettes
vignettes/per_sample_correlation_beta.png
vignettes/per_sample_correlation_rank.png
vignettes/read_and_normalize450K.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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