Title: Fast wavelet based functional models for transcriptome analysis with tiling arrays
Authors: Clement, Lieven ×
De Beuf, Kristof
Thas, Olivier
Vuylsteke, Marnik
Irizarry, Rafael A.
Crainiceanu, Ciprian #
Issue Date: Sep-2010
Publisher: Institute of Mathematical Statistics
Series Title: Annals of Applied Statistics issue:submitted
Abstract: For a better understanding of the biology of an organism a complete description is needed of all regions of the genome that are actively transcribed. Tiling arrays are used for this purpose. Such arrays
allow the discovery of novel transcripts and the assessment of differential expression between two or more experimental conditions such
as genotype, treatment, tissue, etc. In tiling array literature many
efforts are devoted to transcript discovery, whereas more recent developments also focus on differential expression. To our knowledge,
however, no methods for tiling arrays have been described that can
simultaneously assess transcript discovery and identify differentially
expressed transcripts. In this paper, we adopt the wavelet based functional mixed model of Morris and Carroll (2006) to the context of
tiling arrays. The high dimensionality of the data triggered us to
avoid inference based on Bayesian MCMC methods. Instead, we introduce an empirical Bayes method, which is a leap forward in terms
of numerical simplicity. A simulation study and a case study illustrate
that our approach is well suited for the simultaneous assessment of
transcript discovery and differential expression, and it outperforms
methods that accomplish only one of these tasks.
ISSN: 1932-6157
Publication status: submitted
KU Leuven publication type: IT
Appears in Collections:Non-KU Leuven Association publications
× corresponding author
# (joint) last author

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