Illumina WG-6 BeadChip strips should be normalized separately (2009)
Shi, Wei, Banerjee, Ashish, Ritchie, Matthew E, Gerondakis, Steve, Smyth, Gordon K
Abstract Background Illumina Sentrix-6 Whole-Genome Expression BeadChips are relatively new microarray platforms which have been used in many microarray studies in the past few years. These Chips...
Ling, King-Hwa, Hewitt, Chelsee A, Beissbarth, Tim, Hyde, Lavinia, Banerjee, Kakoli, Cheah, Pike-See, ...
Abstract Background Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at...
Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Background correction is an important preprocessing step for microarray data that attempts to adjust the data for the ambient intensity surrounding each feature. The “normexp” method models the...
Testing significance relative to a fold-change threshold is a TREAT (2009)
McCarthy, Davis J., Smyth, Gordon K.
Motivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential...
Robust Frequency Estimation Using Elemental Sets ∗ (2008)
Gordon K. Smyth, Douglas M. Hawkins
The extraction of sinusoidal signals from time-series data is a classic problem of ongoing interest in the statistics and signal processing literatures. Obtaining least squares estimates is difficult...
Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland (2008)
Barker, Holly E, Smyth, Gordon K, Wettenhall, James, Ward, Teresa A, Bath, Mary L, Lindeman, Geoffrey J, ...
Abstract Background The transcription factor DEAF-1 has been identified as a high affinity binding partner of the LIM-only protein LMO4 that plays important roles in mammary gland development and...
Integrative analysis of RUNX1 downstream pathways and target genes (2008)
Michaud, Joëlle, Simpson, Ken M, Escher, Robert, Buchet-Poyau, Karine, Beissbarth, Tim, Carmichael, Catherine, ...
Abstract Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible...
Moderated Statistical Tests for Assessing Differences in Tag Abundance (2008)
Mark D. Robinson, Gordon K. Smyth, Prof David Rocke
Motivation: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologiesfor measuring gene expression on agenomic scale, without the...
Polycomb Repressive Complex 2 (PRC2) Restricts Hematopoietic Stem Cell Activity (2008)
Ian J. Majewski, Marnie E. Blewitt, Edward J. McManus, Melanie Bahlo, Adrienne A. Hilton, ...
Polycomb group proteins are transcriptional repressors that play a central role in the establishment and maintenance of gene expression patterns during development. Using mice with an...
Evaluation of Tweedie exponential dispersion model densities by Fourier inversion (2008)
Dunn, Peter K., Smyth, Gordon K.
[Abstract]: The Tweedie family of distributions is a family of exponential dispersion models with power variance functions V (μ) = μ^p for p not between (0, 1). These distri- butions do not...
Evaluation of Tweedie exponential dispersion model densities by Fourier inversion (2008)
Dunn, Peter K., Smyth, Gordon K.
[Abstract]: The Tweedie family of distributions is a family of exponential dispersion models with power variance functions V (μ) = μ^p for p not between (0, 1). These distri- butions do not...
Small-sample estimation of negative binomial dispersion, with applications to SAGE data (2008)
Robinson, Mark D., Smyth, Gordon K.
We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of the negative binomial distribution and compare its performance, in terms of bias, to various...
Evaluation of Tweedie exponential dispersion model densities by Fourier inversion (2008)
Dunn, Peter K., Smyth, Gordon K.
[Abstract]: The Tweedie family of distributions is a family of exponential dispersion models with power variance functions V (μ) = μ^p for p not between (0, 1). These distri- butions do not...
Saddlepoint Approximations for Extended Poisson Process Models (2007)
Heather Podlich Gordon, Gordon K. Smyth
this paper that the saddlepoint approximation to the probabilities of a state-dependent birth process can provide such a solution. Comparisons will be made with the exact probability solution, and...
Robust Frequency Estimation Using Elemental Sets (2007)
Gordon K. Smyth, Douglas M. Hawkins
The extraction of sinusoidal signals from time-series data has attracted enormous attention in the statistics and signal processing literatures. A closely related problem is that of fitting...
Pearson’s Goodness of Fit Statistic as a Score Test Statistic ∗ (2007)
For any generalized linear model, the Pearson goodness of fit statistic is the score test statistic for testing the current model against the saturated model. The relationship between the Pearson...
Gordon K. Smyth, Melanie Cox, Andrew Moss
Abstract: A method a trend analysis is described for environmental data which accommodates outliers, detection limits, seasonal eects, covariates and long term nonlinear trends.
REGRESSION ANALYSIS OF QUANTITY DATA WITH EXACT ZEROES (2007)
Measurements of the magnitude or duration of physical phenomenon have the property that they are positive and continuous, except for the possibility of exact zeroes when the phenomenon does not...
A comparison of background correction methods for two-colour microarrays (2007)
Ritchie, Matthew E., Silver, Jeremy, Oshlack, Alicia, Holmes, Melissa, Diyagama, Dileepa, Holloway, Andrew, ...
Motivation: Microarray data must be background corrected to remove the effects of non-specific binding or spatial heterogeneity across the array, but this practice typically causes other problems...
Using DNA microarrays to study gene expression in closely related species (2007)
Oshlack, Alicia, Chabot, Adrien E., Smyth, Gordon K., Gilad, Yoav
Motivation: Comparisons of gene expression levels within and between species have become a central tool in the study of the genetic basis for phenotypic variation, as well as in the study of the...
Oshlack, Alicia, Emslie, Dianne, Corcoran, Lynn M, Smyth, Gordon K
Abstract Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct...
Moderated statistical tests for assessing differences in tag abundance (2007)
Robinson, Mark D., Smyth, Gordon K.
Motivation: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the...
Holloway, Andrew J, Oshlack, Alicia, Diyagama, Dileepa S, Bowtell, David DL, Smyth, Gordon K
Abstract Background Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity (2006)
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Abstract Background Signal transducer and activator of transcription (STAT) proteins are key regulators of gene expression in response to the interferon (IFN) family of anti-viral and anti-microbial...
Empirical array quality weights in the analysis of microarray data (2006)
Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, Van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, ...
Abstract Background Assessment of array quality is an essential step in the analysis of data from microarray experiments. Once detected, less reliable arrays are typically excluded or "filtered" from...
BMC Bioinformatics BioMed Central Methodology article (2006)
Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David Dl Bowtell, Gordon K Smyth, Gordon K Smyth
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
affylmGUI: a graphical user interface for linear modeling of single channel microarray data (2006)
Wettenhall, James M., Simpson, Ken M., Satterley, Keith, Smyth, Gordon K.
Summary: affylmGUI is a graphical user interface (GUI) to an integrated workflow for Affymetrix microarray data. The user is able to proceed from raw data (CEL files) to QC and pre-processing, and...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Gordon K. Smyth, Joëlle Michaud, Hamish S. Scott
Motivation. Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting...
Limma: linear models for microarray data (2005)
Gordon K. Smyth, Matthew Ritchie, Natalie Thorne, James Wettenhall
This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.
Gene Expression, James M. Wettenhall, Ken M. Simpson, Keith Satterley, Gordon K. Smyth
single channel microarray data
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries (2005)
Beißbarth, Tim, Tye-Din, Jason A., Smyth, Gordon K., Speed, Terence P., Anderson, Robert P.
Motivation: T-cell response to peptides bound on MHC Class I or Class II molecules is essential for immune recognition of pathogens. T-cells are activated by specific peptide epitopes that are...
Smyth, Gordon K., Michaud, Joëlle, Scott, Hamish S.
Motivation: Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting...
Smyth, Gordon K., Michaud, Joëlle, Scott, Hamish S.
Motivation: Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting...
Series evaluation of Tweedie exponential dispersion model densities (2005)
Dunn, Peter K., Smyth, Gordon K.
Exponential dispersion models, which are linear exponential families with a dispersion parameter, are the prototype response distributions for generalized linear models. The Tweedie family comprises...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential...
The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential...
The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential...
The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Gordon K. Smyth, Gordon K. Smyth
may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of...
The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lönnstedt and Speed (2002) derived an expression for the posterior odds of differential...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
limmaGUI: A graphical user interface for linear modeling of microarray data (2004)
Wettenhall, James M., Smyth, Gordon K.
Summary: limmaGUI is a graphical user interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of...
limmaGUI: a graphical user interface for linear modeling of microarray data (2004)
Wettenhall, James M., Smyth, Gordon K.
Summary: limmaGUI is a Graphical User Interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of...
Statistical modeling of sequencing errors in SAGE libraries (2004)
Beißbarth, Tim, Hyde, Lavinia, Smyth, Gordon K., Job, Chris, Boon, Wee-Ming, Tan, Seong-Seng, ...
Motivation: Sequencing errors may bias the gene expression measurements made by Serial Analysis of Gene Expression (SAGE). They may introduce non-existent tags at low abundance and decrease the real...
limmaGUI: a graphical user interface for linear modeling of microarray data (2004)
Wettenhall, James M., Smyth, Gordon K.
Summary: limmaGUI is a Graphical User Interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of...
Semi-parametric extended Poisson process models for count data (2004)
Podlich, Heather M., Faddy, Malcolm J., Smyth, Gordon K.
A general framework for the analysis of count data (with covariates) is proposed using formulations for the transition rates of a state-dependent birth process. The form for the transition rates...
Statistical issues in cDNA microarray data analysis (2003)
Gordon K. Smyth, Yee Hwa Yang, Terry Speed
Statistical considerations are frequently to the fore in the analysis of microarray data, as researchers sift through massive amounts of data and adjust for various sources of variability in order to...
Statistical issues in cDNA microarray data analysis (2003)
Gordon K. Smyth, Yee Hwa Yang, Terry Speed
Statistical considerations are frequently to the fore in the analysis of microarray data, as researchers sift through massive amounts of data and adjust for various sources of variability in order to...
Fitting tweedie’s compound poisson model to insurance claims data: dispersion modelling (2002)
We reconsider the problem of producing fair and accurate taris based on aggregated insurance data giving numbers of claims and total costs for the claims. Jrgensen and de Souza (Scand. Actuarial J.,...
Exact and approximate REML for heteroscedastic regression (2001)
Smyth, Gordon K., Huele, A. Frederik, Verbyla, Arunas P.
Exact REML for heteroscedastic linear models is compared with a number of approximate REML methods which have been proposed in the literature, especially with the methods proposed by Lee and Nelder...
Exact and approximate REML for heteroscedastic regression (2001)
Smyth, Gordon K., Huele, A. Frederik, Verbyla, Arunas P.
Exact REML for heteroscedastic linear models is compared with a number of approximate REML methods which have been proposed in the literature, especially with the methods proposed by Lee and Nelder...
Randomized Quantile Residuals. (1998)
Dunn, Peter K., Smyth, Gordon K.
In this paper we give a general definition of residuals for regression models with independent responses. Our definition produces residuals which are exactly normal, apart from sampling variability...
Predicting Ship Fuel Consumption: Update. (1997)
Schrady, David A., Smyth, Gordon K., Vassian, Robert B.
This report is concerned with the prediction of ship propulsion fuel consumption as a function of ship speed for U.S. Navy combatant and auxiliary ships. Prediction is based on fitting an analytic...
This article describes classical quadrature methods and, more briefly, some of the more advanced methods for which software is widely available. The description of the elementary methods in this...
Polynomial Approximation (1997)
function, and especially on how small the maximum error can be made. Very high order polynomials may be used here if they provide accurate approximations. Very often a function is not approximated...
Employing Symmetry Constraints for Improved Frequency Estimation by Eigenanalysis Methods (1997)
The problem of extracting sinusoid signals from noisy observations made at equally spaced times is considered. Eigenanalysis methods, such as Pisarenko's method and the extended Prony method,...
Randomized Quantile Residuals (1996)
In this paper we give a general definition of residuals for regression models with independent responses. Our definition produces residuals which are exactly normal, apart from sampling variability...
A conditional likelihood approach to REML in Generalized Linear Models (1995)
Gordon K. Smyth, Arunas P. Verbyla
Residual maximum likelihood estimation (REML) is often preferred to maximum likelihood estimation as a method of estimating covariance parameters in linear models because it takes account of the loss...
A note on modelling cross-correlations: Hyperbolic secant regression (1994)
The problem of determining if a bivariate normal correlation changes with respect to time or some other covariate is considered. It is assumed that the means and standard deviations of the normal...
Empirical array quality weights in the analysis of microarray data
Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, Van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, ...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Peart, Melissa J., Smyth, Gordon K., Van Laar, Ryan K., Bowtell, David D., Richon, Victoria M., Marks, Paul A., ...
Histone deacetylase inhibitors (HDACis) inhibit tumor cell growth and survival, possibly through their ability to regulate the expression of specific proliferative and/or apoptotic genes. However,...
Empirical array quality weights in the analysis of microarray data
Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, Van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, ...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Oshlack, Alicia, Emslie, Dianne, Corcoran, Lynn M, Smyth, Gordon K
A new normalization method is described for use in specialized boutique arrays which contain a subset of genes selected to test particular biological functions.
Integrative analysis of RUNX1 downstream pathways and target genes
Michaud, Joëlle, Simpson, Ken M, Escher, Robert, Buchet-Poyau, Karine, Beissbarth, Tim, Carmichael, Catherine, ...
Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland
Barker, Holly E, Smyth, Gordon K, Wettenhall, James, Ward, Teresa A, Bath, Mary L, Lindeman, Geoffrey J, ...
Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures
Blekhman, Ran, Oshlack, Alicia, Chabot, Adrien E., Smyth, Gordon K., Gilad, Yoav
Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes in which...
Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures
Blekhman, Ran, Oshlack, Alicia, Chabot, Adrien E., Smyth, Gordon K., Gilad, Yoav
Berkovic, Samuel F., Dibbens, Leanne M., Oshlack, Alicia, Silver, Jeremy D., Katerelos, Marina, Vears, Danya F., ...
Action myoclonus-renal failure syndrome (AMRF) is an autosomal-recessive disorder with the remarkable combination of focal glomerulosclerosis, frequently with glomerular collapse, and progressive...
Polycomb Repressive Complex 2 (PRC2) Restricts Hematopoietic Stem Cell Activity
Majewski, Ian J, Blewitt, Marnie E, De Graaf, Carolyn A, McManus, Edward J, Bahlo, Melanie, Hilton, Adrienne A, ...
Polycomb group proteins are transcriptional repressors that play a central role in the establishment and maintenance of gene expression patterns during development. Using mice with an...
Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Background correction is an important preprocessing step for microarray data that attempts to adjust the data for the ambient intensity surrounding each feature. The “normexp” method models the...
Testing significance relative to a fold-change threshold is a TREAT
McCarthy, Davis J., Smyth, Gordon K.
Motivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential...
The molecular signature of CD8+ T cells undergoing deletional tolerance
Parish, Ian A., Rao, Sudha, Smyth, Gordon K., Juelich, Torsten, Denyer, Gareth S., Davey, Gayle M., ...
Peripheral tolerance induction is critical for the maintenance of self-tolerance and can be mediated by immunoregulatory T cells or by direct induction of T-cell anergy or deletion. Although the...
Molecular dissection of the pea shoot apical meristem*
Liang, Dacheng, Wong, Chui E., Singh, Mohan B., Beveridge, Christine A., Phipson, Belinda, Smyth, Gordon K., ...
The shoot apical meristem (SAM) is responsible for the development of all the above-ground parts of a plant. Our understanding of the SAM at the molecular level is incomplete. This study investigates...