R/BHC: fast Bayesian hierarchical clustering for microarray data.
BACKGROUND
Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained.


RESULTS
We present an R/Bioconductor port of a fast novel algorithm for Bayesian agglomerative hierarchical clustering and demonstrate its use in clustering gene expression microarray data. The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge.


CONCLUSIONS
Biologically plausible results are presented from a well studied data set: expression profiles of A. thaliana subjected to a variety of biotic and abiotic stresses. Our method avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric.
Savage
Richard S
RS
Systems Biology Centre, University of Warwick, Coventry House, Coventry CV47AL, UK. r.s.savage@warwick.ac.uk
Heller
Katherine
K
Xu
Yang
Y
Ghahramani
Zoubin
Z
Truman
William M
WM
Grant
Murray
M
Denby
Katherine J
KJ
Wild
David L
DL
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001499:Bayes Theorem; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D012985:Software Design; D013997:Time Factors