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iBATCGH: Integrative Bayesian Analysis of Transcriptomic and CGH Data

  • Alberto Cassese
  • Michele Guindani
  • Marina VannucciEmail author
Conference paper
Part of the Abel Symposia book series (ABEL, volume 11)

Abstract

We describe a method for the integration of high-throughput data from different sources. More specifically, iBATCGH is a package for the integrative analysis of transcriptomic and genomic data, based on a hierarchical Bayesian model. Through the specification of a measurement error model we relate the gene expression levels to latent copy number states which, in turn, are related to the observed surrogate CGH measurement via a hidden Markov model. Selection of relevant associations is performed employing variable selection priors that explicitly incorporate dependence information across adjacent copy number states. Posterior inference is carried out through Markov chain Monte Carlo techniques that efficiently explores the space of all possible associations. In this chapter we review the model and present the functions provided in iBATCGH, an R package based on a C implementation of the inferential algorithm. Lastly, we illustrate the method via a case study on ovarian cancer.

Keywords

Hide Markov Model Comparative Genomic Hybridization Betulinic Acid Lung Squamous Cell Carcinoma Measurement Error Model 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Alberto Cassese
    • 1
  • Michele Guindani
    • 2
  • Marina Vannucci
    • 3
    Email author
  1. 1.Maastricht UniversityMaastrichtThe Netherlands
  2. 2.UT MD Anderson Cancer CenterHoustonUSA
  3. 3.Department of StatisticsRice UniversityHoustonUSA

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