Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments

Data variability can be important in microarray data analysis. Thus, when clustering gene expression profiles, it could be judicious to make use of repeated data. In this paper, the problem of analysing repeated data in the model-based cluster analysis context is considered. Linear mixed models are...

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Bibliographic Details
Published in:Statistical modelling 2005-10, Vol.5 (3), p.243-267
Main Authors: Celeux, Gilles, Martin, Olivier, Lavergne, Christian
Format: Article
Language:English
Subjects:
Algorithms
Cluster analysis
Clustering
Data analysis
Experiments
Gene expression
Mathematics
Monte Carlo simulation
Software
Statistics
Statistics Theory
Studies
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Summary:Data variability can be important in microarray data analysis. Thus, when clustering gene expression profiles, it could be judicious to make use of repeated data. In this paper, the problem of analysing repeated data in the model-based cluster analysis context is considered. Linear mixed models are chosen to take into account data variability and mixture of these models are considered. This leads to a large range of possible models depending on the assumptions made on both the covariance structure of the observations and the mixture model. The maximum likelihood estimation of this family of models through the EM algorithm is presented. The problem of selecting a particular mixture of linear mixed models is considered using penalized likelihood criteria. Illustrative Monte Carlo experiments are presented and an application to the clustering of gene expression profiles is detailed. All those experiments highlight the interest of linear mixed model mixtures to take into account data variability in a cluster analysis context.
ISSN:1471-082X
1477-0342
DOI:10.1191/1471082X05st096oa