alexa Interpretation of ANOVA models for microarray data using PCA.
Toxicology

Toxicology

Journal of Drug Metabolism & Toxicology

Author(s): de Haan JR, Wehrens R, Bauerschmidt S, Piek E, van Schaik RC, , de Haan JR, Wehrens R, Bauerschmidt S, Piek E, van Schaik RC,

Abstract Share this page

Abstract MOTIVATION: ANOVA is a technique, which is frequently used in the analysis of microarray data, e.g. to assess the significance of treatment effects, and to select interesting genes based on P-values. However, it does not give information about what exactly is causing the effect. Our purpose is to improve the interpretation of the results from ANOVA on large microarray datasets, by applying PCA on the individual variance components. Interaction effects can be visualized by biplots, showing genes and variables in one plot, providing insight in the effect of e.g. treatment or time on gene expression. Because ANOVA has removed uninteresting sources of variance, the results are much more interpretable than without ANOVA. Moreover, the combination of ANOVA and PCA provides a simple way to select genes, based on the interactions of interest. RESULTS: It is shown that the components from an ANOVA model can be summarized and visualized with PCA, which improves the interpretability of the models. The method is applied to a real time-course gene expression dataset of mesenchymal stem cells. The dataset was designed to investigate the effect of different treatments on osteogenesis. The biplots generated with the algorithm give specific information about the effects of specific treatments on genes over time. These results are in agreement with the literature. The biological validation with GO annotation from the genes present in the selections shows that biologically relevant groups of genes are selected. AVAILABILITY: R code with the implementation of the method for this dataset is available from http://www.cac.science.ru.nl under the heading "Software". This article was published in Bioinformatics and referenced in Journal of Drug Metabolism & Toxicology

Relevant Expert PPTs

Relevant Speaker PPTs

Recommended Conferences

  • European Biopharma Congress
    November 16-17, Vienna, Austria

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

[email protected]

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Business & Management Journals

Ronald

[email protected]

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

[email protected]

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

[email protected]

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

[email protected]

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

[email protected]

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

[email protected]

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

[email protected]

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

[email protected]

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

[email protected]

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

[email protected]

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

[email protected]

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

[email protected]

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

[email protected]

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

[email protected]

1-702-714-7001 Extn: 9042

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords