Skip Navigation


Bioinformatics Advance Access originally published online on January 17, 2006
Bioinformatics 2006 22(7):808-814; doi:10.1093/bioinformatics/btk052
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/7/808    most recent
btk052v1
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
Right arrow Search for citing articles in:
ISI Web of Science (12)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Seo, J.
Right arrow Articles by Hoffman, E. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Seo, J.
Right arrow Articles by Hoffman, E. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An interactive power analysis tool for microarray hypothesis testing and generation

Jinwook Seo *, Heather Gordish-Dressman and Eric P. Hoffman

Research Center for Genetic Medicine, Children's National Medical Center Washington DC 20010, USA

*To whom correspondence should be addressed.

Motivation: Human clinical projects typically require a priori statistical power analyses. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies integrated into our public domain HCE 3.5 software package. We then sought to determine if probe set algorithms or organism type strongly influenced power analysis results.

Results: The HCE 3.5 power analysis tool was designed to import any pre-existing Affymetrix microarray project, and interactively test the effects of user-defined definitions of {alpha} (significance), ß (1 – power), sample size and effect size. The tool generates a filter for all probe sets or more focused ontology-based subsets, with or without noise filters that can be used to limit analyses of a future project to appropriately powered probe sets. We studied projects from three organisms (Arabidopsis, rat, human), and three probe set algorithms (MAS5.0, RMA, dChip PM/MM). We found large differences in power results based on probe set algorithm selection and noise filters. RMA provided high sensitivity for low numbers of arrays, but this came at a cost of high false positive results (24% false positive in the human project studied). Our data suggest that a priori power calculations are important for both experimental design in hypothesis testing and hypothesis generation, as well as for the selection of optimized data analysis parameters.

Availability: The Hierarchical Clustering Explorer 3.5 with the interactive power analysis functions is available at www.cs.umd.edu/hcil/hce or www.cnmcresearch.org/bioinformatics.

Contact: jseo{at}cnmcresearch.org

Received on November 11, 2005; revised on December 23, 2005; accepted on January 9, 2006

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
 Plant Cell PhysiolHome page
N. Mitsuda and M. Ohme-Takagi
Functional Analysis of Transcription Factors in Arabidopsis
Plant Cell Physiol., July 1, 2009; 50(7): 1232 - 1248.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Krushevskaya, H. Peterson, J. Reimand, M. Kull, and J. Vilo
VisHiC--hierarchical functional enrichment analysis of microarray data
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W587 - W592.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Y. Kotliarov, S. Kotliarova, N. Charong, A. Li, J. Walling, E. Aquilanti, S. Ahn, M. E. Steed, Q. Su, A. Center, et al.
Correlation Analysis between Single-Nucleotide Polymorphism and Expression Arrays in Gliomas Identifies Potentially Relevant Target Genes
Cancer Res., February 15, 2009; 69(4): 1596 - 1603.
[Abstract] [Full Text] [PDF]

Home page
 Arch Otolaryngol Head Neck SurgHome page
X. Wu, S. Ghimbovschi, P. K. Aujla, M. C. Rose, and M. T. Pena
Expression Profiling of Inflammatory Mediators in Pediatric Sinus Mucosa
Arch Otolaryngol Head Neck Surg, January 1, 2009; 135(1): 65 - 72.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
F. Cordero, M. Botta, and R. A. Calogero
Microarray data analysis and mining approaches
Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
T. S. Mehta, S. O. Zakharkin, G. L. Gadbury, and D. B. Allison
Epistemological issues in omics and high-dimensional biology: give the people what they want
Physiol Genomics, December 13, 2006; 28(1): 24 - 32.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Lechno-Yossef, Q. Fan, S. Ehira, N. Sato, and C. P. Wolk
Mutations in Four Regulatory Genes Have Interrelated Effects on Heterocyst Maturation in Anabaena sp. Strain PCC 7120
J. Bacteriol., November 1, 2006; 188(21): 7387 - 7395.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
J.-J. Park, J. R. Berggren, M. W. Hulver, J. A Houmard, and E. P. Hoffman
GRB14, GPD1, and GDF8 as potential network collaborators in weight loss-induced improvements in insulin action in human skeletal muscle
Physiol Genomics, October 11, 2006; 27(2): 114 - 121.
[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.