Skip Navigation


Bioinformatics Advance Access originally published online on May 8, 2008
Bioinformatics 2008 24(13):1547-1548; doi:10.1093/bioinformatics/btn224
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
24/13/1547    most recent
btn224v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (9)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Du, P.
Right arrow Articles by Lin, S. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Du, P.
Right arrow Articles by Lin, S. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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 *, Warren A. Kibbe and Simon M. Lin

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

*To whom correspondence should be addressed.


  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: dupan{at}northwestern.edu

Associate Editor: Joaquin Dopazo

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Virol.Home page
T. Peng, J. Zhu, A. Klock, K. Phasouk, M.-L. Huang, D. M. Koelle, A. Wald, and L. Corey
Evasion of the Mucosal Innate Immune System by Herpes Simplex Virus Type 2
J. Virol., December 1, 2009; 83(23): 12559 - 12568.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
A. J. Jasinska, S. Service, O.-w. Choi, J. DeYoung, O. Grujic, S.-y. Kong, M. J. Jorgensen, J. Bailey, S. Breidenthal, L. A. Fairbanks, et al.
Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits
Hum. Mol. Genet., November 15, 2009; 18(22): 4415 - 4427.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Microbiol. Rev.Home page
M. B. Miller and Y.-W. Tang
Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology
Clin. Microbiol. Rev., October 1, 2009; 22(4): 611 - 633.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. E. Ritchie, B. S. Carvalho, K. N. Hetrick, S. Tavare, and R. A. Irizarry
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Bioinformatics, October 1, 2009; 25(19): 2621 - 2623.
[Abstract] [Full Text] [PDF]

Home page
 StrokeHome page
C. Shi, I. A. Awad, N. Jafari, S. Lin, P. Du, Z. A. Hage, R. Shenkar, C. C. Getch, M. Bredel, H. H. Batjer, et al.
Genomics of Human Intracranial Aneurysm Wall
Stroke, April 1, 2009; 40(4): 1252 - 1261.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Xie, X. Wang, and M. Story
Statistical methods of background correction for Illumina BeadArray data
Bioinformatics, March 15, 2009; 25(6): 751 - 757.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. L. Asare, Z. Gao, V. J. Carey, R. Wang, and V. Seyfert-Margolis
Power enhancement via multivariate outlier testing with gene expression arrays
Bioinformatics, January 1, 2009; 25(1): 48 - 53.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
F. Fang, A. J. Flegler, P. Du, S. Lin, and C. V. Clevenger
Expression of Cyclophilin B is Associated with Malignant Progression and Regulation of Genes Implicated in the Pathogenesis of Breast Cancer
Am. J. Pathol., January 1, 2009; 174(1): 297 - 308.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.