lumidat-package: Preprocess Illumina Gene Expression iDAT files.

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

Description

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 [1] to simultaneously improve noise and bias, via the lumi, or limma pipelines. We have made every effort to reproduce the GenomeStudio output [2], down to the Detection P-Value calculation, the order of the rows, the background correction procedure, the file headers and ProbeID naming, and sample naming.

Details

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 [3], 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 the crlmm package can read them.

Key functions

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 NuID [4].

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.

list_illumina_manifest_files and download_illumina_manifest_file allow you to query and download the required array manifest files.

Array manifest files

Array manifest files are required, and can be downloaded from Illumina [5], [6]. 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 list_illumina_manifest_files, and download_illumina_manifest_file.

Analysis pipeline

##

Author(s)

Mark Cowley <[e-mail]>, with contributions from Mark Pinese and David Eby

References

[1] 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)
[2] Genome Studio Gene Expression Module User Guide, version 1.0, Illumina
[3] http://genepattern.broadinstitute.org
[4] 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)
[5] http://www.switchtoi.com/annotationfiles.ilmn
[6] http://www.switchtoi.com/annotationprevfiles.ilmn

See Also

preprocess.illumina.idat, lumiR.idat, read.ilmn

Examples

## Not run: example(preprocess.illumina.idat)
## Not run: example(lumiR.idat)
## Not run: example(read.ilmn.idat)

drmjc/lumidat documentation built on May 15, 2019, 2:23 p.m.