This package enables the decryption, and preprocessing of
lllumina gene expression iDAT files (aka version 1 iDAT
files). Previously, the only option that Illumina gene
expression users had was to rely upon a miroarray 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  to simultaneously improve noise and
bias, via the
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, the file headers and ProbeID naming, and
The bulk of the work is carried out by a Java program, which aims to reproduce the behaviour of Illumina GenomeStudio, thereby producing “Sample Probe Profile.txt” and “Control Probe Profile.txt” files. This Java program is initially based on the IlluminaExpressionFileCreator GenePattern module , created by the Broad Institute (most of the coding done by David Eby).
This package will NOT read iDAT files from Illumina
Infinium SNP arrays (aka Version 3 iDAT files); however
crlmm package can read them.
preprocess.illumina.idat provides a number
of options for reading iDAT files, including background
correction, summarisation at the gene-level. Unlike
GenomeStudio, it provides greater control over how the
gene-level summarisation is performed, and provides a
number of different options for naming probes, including
lumiR.idat provides a replacement for
lumiR, and allows users to use the
lumi pipeline starting with iDAT files.
read.ilmn.idat provides a replacement for
read.ilmn, and allows users to use
the limma pipeline starting with iDAT files.
download_illumina_manifest_file allow you
to query and download the required array manifest files.
Array manifest files are required, and can be downloaded
from Illumina , . These files describe each of the
probes on the array, including the probe sequence, as
well as probe-level annotations. See
preprocess.illumina.idat for more info. To
make this easier, we have added
Mark Cowley <[email protected]>, with contributions from Mark Pinese and David Eby
 Shi, W., Oshlack, A., & Smyth, G. K. (2010).
Optimizing the noise versus bias trade-off for Illumina
whole genome expression BeadChips Nucleic acids research,
38(22), e204. (doi:10.1093/nar/gkq871)
 Genome Studio Gene Expression Module User Guide, version 1.0, Illumina
 Du, P., Kibbe, W. A., & Lin, S. M. (2007). nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays Biol Direct, 2, 16. (doi:10.1186/1745-6150-2-16)
1 2 3
## Not run: example(preprocess.illumina.idat) ## Not run: example(lumiR.idat) ## Not run: example(read.ilmn.idat)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.