drmjc/lumidat: Methods for importing Illumina gene expression iDAT files

This package enables the decryption, and preprocessing of Illumina gene expression iDAT files (aka version 1 iDAT files). Previously, the only option that Illumina gene expression customers had was to rely upon a microarray core facility with access to an Illumina Scanner and a copy of Illumina BeadStudio, or GenomeStudio to pre-process the array data. Our intention is to allow users to pre-process their probe-level Illumina data using this software, thereby enabling them to choose from the collection of sophisticated normalisation and pre-processing procedures, which have recently been demonstrated by Shi et al, 2010 to simultaneously improve noise and bias, via the \emph{lumi}, or \emph{limma} pipelines. We have made every effort to reproduce the GenomeStudio output, down to the Detection P-Value calculation, the order of the rows, the background correction procedure (which is only applied to gene-probes), the file formats and names.

Getting started

Package details

AuthorMark Cowley
MaintainerMark Cowley <[email protected]>
Licensefile LICENSE
Version1.2.3
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("drmjc/lumidat")
drmjc/lumidat documentation built on May 15, 2019, 2:23 p.m.