Skip Navigation


Bioinformatics Advance Access originally published online on October 25, 2008
Bioinformatics 2008 24(24):2921-2922; doi:10.1093/bioinformatics/btn557
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
24/24/2921    most recent
btn557v1
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 ISI Web of Science
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
Google Scholar
Right arrow Articles by Cairns, J. M.
Right arrow Articles by Lynch, A. G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Cairns, J. M.
Right arrow Articles by Lynch, A. G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

BASH: a tool for managing BeadArray spatial artefacts

J. M. Cairns , M. J. Dunning , M. E. Ritchie , R. Russell and A. G. Lynch *

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

*To whom correspondence should be addressed.


  Abstract

Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses.

Availability: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org

Contact: andy.lynch{at}cancer.org.uk

Supplementary information: Additional information and a vignette are included in the beadarray package.

Associate Editor: Martin Bishop

Received on September 17, 2008; revised on October 23, 2008; accepted on October 23, 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
 Nucleic Acids ResHome page
N. L. Barbosa-Morais, M. J. Dunning, S. A. Samarajiwa, J. F. J. Darot, M. E. Ritchie, A. G. Lynch, and S. Tavare
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
Nucleic Acids Res., November 18, 2009; (2009) gkp942v1.
[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]


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.