flowClust: a Bioconductor package for automated gating of flow cytometry data (2009)
Lo, Kenneth, Hahne, Florian, Brinkman, Ryan R, Gottardo, Raphael
Abstract Background As a high-throughput technology that offers rapid quantification of multidimensional characteristics for millions of cells, flow cytometry (FCM) is widely used in health research,...
PICS: Probabilistic Inference for ChIP-seq (2009)
Zhang, Xuekui, Robertson, Gordon, Krzywinski, Martin, Ning, Kaida, Droit, Arnaud, Jones, Steven, ...
ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity,...
Raphael Gottardo, Julian Besag, Matthew Stephens, Alejandro Murua
We describe a probabilistic approach to simultaneous image segmentation and intensity estimation for cDNA microarray experiments. The approach overcomes several limitations of existing methods. In...
Motivation: Inference about differential expression is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular for this type...
Chu, Vu T, Gottardo, Raphael, Raftery, Adrian E, Bumgarner, Roger E, Yeung, Ka
Abstract We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R...
2006b) Quality control and robust estimation of cDNA microarray with replicates (2008)
Raphael Gottardo, Adriane. Raftery, Roger E. Bumgarner
We consider robust estimation of gene intensities from cDNA microarray data with replicates. Several statistical methods for estimating gene intensities from microarrays have been proposed, but...
Combining Mixture Components for Clustering (2008)
Baudry, Jean-Patrick, E. Raftery, Adrian, Celeux, Gilles, Lo, Kenneth, Gottardo, Raphael
Model-based clustering consists of fitting a mixture model to data and identifying each cluster with one of its components. Multivariate normal distributions are typically used. The number of...
Combining Mixture Components for Clustering (2008)
Baudry, Jean-Patrick, E. Raftery, Adrian, Celeux, Gilles, Lo, Kenneth, Gottardo, Raphael
Model-based clustering consists of fitting a mixture model to data and identifying each cluster with one of its components. Multivariate normal distributions are typically used. The number of...
A MESSAGE FROM THE EDITOR (2008)
Christian Robert, Raphael Gottardo
Dear friends and Isba members, as pointed out by Raphael Gottardo below, this is a welcome time for most of us to clean up our desks from the clutter that accumulated over the semester and to get...
A MESSAGE FROM THE EDITOR (2008)
Christian Robert, Raphael Gottardo
Even those of us who took a well deserved break sometimes over the past months are back to work with new duties kicking in, like new courses, new students, new duties, etc. I have had a great summer...
A MESSAGE FROM THE EDITOR (2008)
Christian Robert, Raphael Gottardo
Season Greetings to all ISBA members and ISBA Bulletin readers! I hope that, despite the black clouds accumulating on various horizons, you found the time and stamina for celebration and resourcing...
Raphael Gottardo, Maintainer Raphael Gottardo
Description Estimation of missing values in a matrix by a k-th nearest neighboors algorithm
Description This package contains some simple functions for the analysis of growth curve experiments.
March Title Estimation, Raphael Gottardo, Maintainer Raphael Gottardo
missing value, based on the Euclidian distance or the sample correlation. Then the missing values are replaced by the average of the neighboors. Note that if a row only contains missing values then...
November Title Analysis, Raphael Gottardo
tablished tumors to one of six groups: 0% (control), 0.5%, 1%, 2% and 3%. Tumors in each group were measured at day 0, 3, 7, 10, 14 and 16. Format A matrix, the first column contains the group ids...
Robust Estimation of cDNA Microarray Intensities with Replicates (2007)
Gottardo, Raphael, Raftery, Adrian E., Yeung, Ka Yee, Bumgarner, Roger E.
On-line Changepoint Detection and Parameter Estimation for Genome-wide Transcript Analysis (2007)
Francois Caron, Raphael Gottardo, Arnaud Doucet, François Caron, Raphael Gottardo, Arnaud Doucet
We consider the problem of identifying novel RNA transcripts using tiling arrays. Standard approaches to this problem rely on the calculation of a sliding window statistic or on simple changepoint...
Bayesian Robust Variable and Transformation Selection: A Unified Approach (2007)
Raphael Gottardo, Adrian E. Raftery
We consider the problem of simultaneous variable and transformation selection for linear regression. We propose a fully Bayesian solution to the problem, which allows us to average over all possible...
Flexible empirical Bayes models for differential gene expression (2007)
Lo, Kenneth, Gottardo, Raphael
Motivation: Inference about differential expression is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular for this type...
Probabilistic segmentation and intensity estimation for microarray images (2006)
Raphael Gottardo, Julian Besag, Ro Murua, Matthew Stephens
Algorithms for image segmentation and intensity estimation are crucial to the successful analysis of cDNA microarray experiments but most procedures allow little or no flexibility. Our methods...
Raphael Gottardo, Adrian E. Raftery, Ka Yee Yeung
Summary. We consider the problem of identifying differentially expressed genes under different conditions using gene expression microarrays. Because of the many steps involved in the experimental...
Raphael Gottardo, Adrian E. Raftery, Ka Yee Yeung, Roger E. Bumgarner
We consider the problem of identifying differentially expressed genes under different conditions using cDNA microarrays. Standard statistical methods cannot be used because typically there are...
Probabilistic segmentation and intensity estimation for microarray images (2006)
Gottardo, Raphael, Besag, Julian, Stephens, Matthew, Murua, Alejandro
We describe a probabilistic approach to simultaneous image segmentation and intensity estimation for complementary DNA microarray experiments. The approach overcomes several limitations of existing...
Probabilistic Segmentation and Intensity Estimation for Microarray Images (2005)
Gottardo, Raphael, Besag, Julian, Stephens, Matthew, Murua, Alejandro
We describe a probabilistic approach to simultaneous image segmentation and intensity estimation for cDNA microarray experiments. The approach overcomes several limitations of existing methods. In...
Raphael Gottardo, Maintainer Raphael Gottardo
Description Estimation of missing values in a matrix by a k-th nearest neighboors algorithm
Markov chain Monte Carlo with mixtures of singular distributions (2004)
Raphael Gottardo, Adrian E. Raftery
Markov chain Monte Carlo (MCMC) methods for Bayesian computation are mostly used when the dominating measure is the Lebesgue measure, the counting measure or a product of these. Many Bayesian...
Xie, Gary, Bonner, Carol A, Brettin, Tom, Gottardo, Raphael, Keyhani, Nemat O, Jensen, Roy A
Abstract Background Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous...
Robust estimation of cDNA microarray intensities (2003)
Raphael Gottardo, Adrian E. Raftery, Ka Yee Yeung, Roger E. Bumgarner
10745. Yeung and Bumgarner were supported by NIH-NIDDK grant 5U24DK058813-02. We consider robust estimation of gene intensities from cDNA microarray data with replicates. Several statistical methods...
Statistical analysis of microarray data: a Bayesian approach (2003)
Gottardo, Raphael, Pannucci, James A., Kuske, Cheryl R., Brettin, Thomas
The potential of microarray data is enormous. It allows us to monitor the expression of thousands of genes simultaneously. A common task with microarray is to determine which genes are differentially...
Xie, Gary, Bonner, Carol A, Brettin, Tom, Gottardo, Raphael, Keyhani, Nemat O, Jensen, Roy A
Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated. A seven-gene cluster in Xylella fastidiosa exhibits a sharply delineated low-GC content. This strongly...
Xie, Gary, Bonner, Carol A, Brettin, Tom, Gottardo, Raphael, Keyhani, Nemat O, Jensen, Roy A
Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated. A seven-gene cluster in Xylella fastidiosa exhibits a sharply delineated low-GC content. This strongly...
Model-based analysis of tiling-arrays for ChIP-chip
Johnson, W. Evan, Li, Wei, Meyer, Clifford A., Gottardo, Raphael, Carroll, Jason S., Brown, Myles, ...
We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP)...
Quality Control and Robust Estimation for cDNA Microarrays With Replicates
Gottardo, Raphael, Raftery, Adrian E., Yeung, Ka Yee, Bumgarner, Roger E.
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
Chu, Vu T, Gottardo, Raphael, Raftery, Adrian E, Bumgarner, Roger E, Yeung, Ka Yee
MeV+R provides users with point-and-click access to traditionally command-line-driven tools written in R.