Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year


IMPACT FACTOR 2016: 0.646
5-year IMPACT FACTOR: 1.191

CiteScore 2016: 0.94

SCImago Journal Rank (SJR) 2016: 0.625
Source Normalized Impact per Paper (SNIP) 2016: 0.596

Mathematical Citation Quotient (MCQ) 2016: 0.06

Online
ISSN
1544-6115
See all formats and pricing
More options …
Volume 11, Issue 3 (Apr 2012)

Issues

Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

The practical effect of batch on genomic prediction

Hilary S. Parker / Jeffrey T. Leek
Published Online: 2012-04-16 | DOI: https://doi.org/10.1515/1544-6115.1766

Measurements from microarrays and other high-throughput technologies are susceptible to non-biological artifacts like batch effects. It is known that batch effects can alter or obscure the set of significant results and biological conclusions in high-throughput studies. Here we examine the impact of batch effects on predictors built from genomic technologies. To investigate batch effects, we collected publicly available gene expression measurements with known outcomes, and estimated batches using date. Using these data we show (1) the impact of batch effects on prediction depends on the correlation between outcome and batch in the training data, and (2) removing expression measurements most affected by batch before building predictors may improve the accuracy of those predictors. These results suggest that (1) training sets should be designed to minimize correlation between batches and outcome, and (2) methods for identifying batch-affected probes should be developed to improve prediction results for studies with high correlation between batches and outcome.

Keywords: batch effects; prediction; microarrays; reproducibility; research design

About the article

Published Online: 2012-04-16


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.1515/1544-6115.1766.

Export Citation

©2012 Walter de Gruyter GmbH & Co. KG, Berlin/Boston. Copyright Clearance Center

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Jean-Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W Zanke, Thomas J Hudson, Elana J Fertig, Celia MT Greenwood, and Kasper D Hansen
Genome Biology, 2014, Volume 15, Number 11
[2]
Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, and Elana J. Fertig
Bioinformatics, 2014, Volume 30, Number 19, Page 2757
[3]
Aline Talhouk, Stefan Kommoss, Robertson Mackenzie, Martin Cheung, Samuel Leung, Derek S. Chiu, Steve E. Kalloger, David G. Huntsman, Stephanie Chen, Maria Intermaggio, Jacek Gronwald, Fong C. Chan, Susan J. Ramus, Christian Steidl, David W. Scott, Michael S. Anglesio, and Benjamin Haibe-Kains
PLOS ONE, 2016, Volume 11, Number 4, Page e0153844
[4]
Charlotte Soneson, Sarah Gerster, Mauro Delorenzi, and Shu-Dong Zhang
PLoS ONE, 2014, Volume 9, Number 6, Page e100335
[5]
Nicholas GD Masca, Elizabeth MA Hensor, Victoria R Cornelius, Francesca M Buffa, Helen M Marriott, James M Eales, Michael P Messenger, Amy E Anderson, Chris Boot, Catey Bunce, Robert D Goldin, Jessica Harris, Rod F Hinchliffe, Hiba Junaid, Shaun Kingston, Carmen Martin-Ruiz, Christopher P Nelson, Janet Peacock, Paul T Seed, Bethany Shinkins, Karl J Staples, Jamie Toombs, Adam KA Wright, and M Dawn Teare
eLife, 2015, Volume 4
[6]
Hilary S. Parker, Héctor Corrada Bravo, and Jeffrey T. Leek
PeerJ, 2014, Volume 2, Page e561
[7]
Jung Ae Lee, Kevin K. Dobbin, and Jeongyoun Ahn
Statistics in Medicine, 2014, Volume 33, Number 15, Page 2681

Comments (0)

Please log in or register to comment.
Log in