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Bioinformatics Advance Access published online on May 8, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn224
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

lumi: a pipeline for processing Illumina microarray

Pan Du 1,*, Warren A. Kibbe 1 and Simon M. Lin 1

1Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA

*To whom correspondence should be addressed. Dr. Pan Du, E-mail: dupan{at}northwestern.edu


  Abstract

Summary: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.

Availability: The lumi Bioconductor package, www.bioconductor.org

Contact: Pan Du (dupan{at}northwestern.edu), Warren Kibbe (wakibbe{at}northwestern.edu), Simon Lin (s-lin2{at}northwestern.edu

Associate Editor: Dr. Joaquin Dopazo

Received on December 20, 2007; revised on February 3, 2008; accepted on May 5, 2008

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