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URL: http://www.bioconductor.org/packages/release/bioc/html/gprege.html
Proper Citation: gprege (RRID:SCR_001324)
Description: Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007).
Abbreviations: gprege
Synonyms: Gaussian Process Ranking and Estimation of Gene Expression time-series
Resource Type: software resource
Defining Citation: PMID:21599902
Keywords: differential expression, microarray, preprocessing, time course, bio.tools
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