Document Detail


Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays.
MedLine Citation:
PMID:  18316342     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: Oligonucleotide arrays such as Affymetrix GeneChips use multiple probes, or a probe set, to measure the abundance of mRNA of every gene of interest. Some analysis methods attempt to summarize the multiple observations into one single score before conducting further analysis such as detecting differentially expressed genes (DEG), clustering and classification. However, there is a risk of losing a significant amount of information and consequently reaching inaccurate or even incorrect conclusions during this data reduction. RESULTS: We developed a novel statistical method called robustified multivariate analysis of variance (MANOVA) based on the traditional MANOVA model and permutation test to detect DEG for both one-way and two-way cases. It can be extended to detect some special patterns of gene expression through profile analysis across k (>or=2) populations. The method utilizes probe-level data and requires no assumptions about the distribution of the dataset. We also propose a method of estimating the null distribution using quantile normalization in contrast to the 'pooling' method (Section 3.1). Monte Carlo simulation and real data analysis are conducted to demonstrate the performance of the proposed method comparing with the 'pooling' method and the usual Analysis of Variance (ANOVA) test based on the summarized scores. It is found that the new method successfully detects DEG under desired false discovery rate and is more powerful than the competing method especially when the number of groups is small. AVAILABILITY: The package of robustified MANOVA can be downloaded from http://faculty.ucr.edu/~xpcui/software
Authors:
Jin Xu; Xinping Cui
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2008-03-03
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  24     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2008 Apr 
Date Detail:
Created Date:  2008-04-14     Completed Date:  2008-05-14     Revised Date:  2009-11-04    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1056-62     Citation Subset:  IM    
Affiliation:
Department of Statistics, East China Normal University, Shanghai 200241, China.
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MeSH Terms
Descriptor/Qualifier:
Analysis of Variance
Artifacts*
Data Interpretation, Statistical*
Gene Expression Profiling / methods*
Multivariate Analysis
Oligonucleotide Array Sequence Analysis / methods*
Reproducibility of Results
Sensitivity and Specificity
Software*

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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