Multiple tests of association with biological annotation metadata (2008)
Dudoit, Sandrine, Keleş, Sündüz, Van Der Laan, Mark J.
We propose a general and formal statistical framework for multiple tests of association between known fixed features of a genome and unknown parameters of the distribution of variable features of...
Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation (2007)
Shilane, David, Liang, Richard H., Dudoit, Sandrine
Many statistical inference methods rely upon selection procedures to estimate a parameter of the joint distribution of explanatory and outcome data, such as the regression function. Within the...
Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation (2007)
Shilane, David, Liang, Richard H., Dudoit, Sandrine
Many statistical inference methods rely upon selection procedures to estimate a parameter of the joint distribution of explanatory and outcome data, such as the regression function. Within the...
Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation (2007)
Shilane, David, Liang, Richard H., Dudoit, Sandrine
Many statistical inference methods rely upon selection procedures to estimate a parameter of the joint distribution of explanatory and outcome data, such as the regression function. Within the...
Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation (2007)
Shilane, David, Liang, Richard H., Dudoit, Sandrine
Many statistical inference methods rely upon selection procedures to estimate a parameter of the joint distribution of explanatory and outcome data, such as the regression function. Within the...
Dudoit, Sandrine, Gilbert, Houston N, Van Der Laan, Mark J.
This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates,...
Dudoit, Sandrine, Gilbert, Houston N, Van Der Laan, Mark J.
This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates,...
Dudoit, Sandrine, Gilbert, Houston N, Van Der Laan, Mark J.
This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates,...
Dudoit, Sandrine, Gilbert, Houston N, Van Der Laan, Mark J.
This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates,...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark J.
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark J.
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark J.
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (2006)
Rubin, Daniel, Dudoit, Sandrine, Van Der Laan, Mark J.
Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null...
Shilane, David, Martikainen, Jarno, Dudoit, Sandrine, Ovaska, Seppo
This paper proposes a statistical methodology for comparing the performance of evolutionary computation algorithms. A two-fold sampling scheme for collecting performance data is introduced, and these...
Shilane, David, Martikainen, Jarno, Dudoit, Sandrine, Ovaska, Seppo
This paper proposes a statistical methodology for comparing the performance of evolutionary computation algorithms. A two-fold sampling scheme for collecting performance data is introduced, and these...
Shilane, David, Martikainen, Jarno, Dudoit, Sandrine, Ovaska, Seppo
This paper proposes a statistical methodology for comparing the performance of evolutionary computation algorithms. A two-fold sampling scheme for collecting performance data is introduced, and these...
Shilane, David, Martikainen, Jarno, Dudoit, Sandrine, Ovaska, Seppo
This paper proposes a statistical methodology for comparing the performance of evolutionary computation algorithms. A two-fold sampling scheme for collecting performance data is introduced, and these...
Multiple Tests of Association with Biological Annotation Metadata (2006)
Dudoit, Sandrine, Keles, Sunduz, Van Der Laan, Mark J.
We propose a general and formal statistical framework for the multiple tests of associations between known fixed features of a genome and unknown parameters of the distribution of variable features...
Multiple Tests of Association with Biological Annotation Metadata (2006)
Dudoit, Sandrine, Keles, Sunduz, Van Der Laan, Mark J.
We propose a general and formal statistical framework for the multiple tests of associations between known fixed features of a genome and unknown parameters of the distribution of variable features...
Multiple Tests of Association with Biological Annotation Metadata (2006)
Dudoit, Sandrine, Keles, Sunduz, Van Der Laan, Mark J.
We propose a general and formal statistical framework for the multiple tests of associations between known fixed features of a genome and unknown parameters of the distribution of variable features...
Multiple Tests of Association with Biological Annotation Metadata (2006)
Dudoit, Sandrine, Keles, Sunduz, Van Der Laan, Mark J.
We propose a general and formal statistical framework for the multiple tests of associations between known fixed features of a genome and unknown parameters of the distribution of variable features...
A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing (2005)
Wang, Yan, Zhao, Lue Ping, Dudoit, Sandrine
High-throughput genotyping technologies for single nucleotide polymorphisms (SNP) have enabled the recent completion of the International HapMap Project (Phase I), which has stimulated much interest...
A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing (2005)
Wang, Yan, Zhao, Lue Ping, Dudoit, Sandrine
High-throughput genotyping technologies for single nucleotide polymorphisms (SNP) have enabled the recent completion of the International HapMap Project (Phase I), which has stimulated much interest...
A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing (2005)
Wang, Yan, Zhao, Lue Ping, Dudoit, Sandrine
High-throughput genotyping technologies for single nucleotide polymorphisms (SNP) have enabled the recent completion of the International HapMap Project (Phase I), which has stimulated much interest...
A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing (2005)
Wang, Yan, Zhao, Lue Ping, Dudoit, Sandrine
High-throughput genotyping technologies for single nucleotide polymorphisms (SNP) have enabled the recent completion of the International HapMap Project (Phase I), which has stimulated much interest...
Pollard, Katherine S., Birkner, Merrill D., Van Der Laan, Mark J., Dudoit, Sandrine
Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We...
Pollard, Katherine S., Birkner, Merrill D., Van Der Laan, Mark J., Dudoit, Sandrine
Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We...
Pollard, Katherine S., Birkner, Merrill D., Van Der Laan, Mark J., Dudoit, Sandrine
Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We...
Pollard, Katherine S., Birkner, Merrill D., Van Der Laan, Mark J., Dudoit, Sandrine
Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We...
Colon Cancer Prognosis Prediction by Gene Expression Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Materials and Methods. Tumour (T)...
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on non-neoplastic mucosa microarray gene expression measures, in stage II colon cancer patients. Materials and Methods....
Colon Cancer Prognosis Prediction by Gene Expression Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Materials and Methods. Tumour (T)...
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on non-neoplastic mucosa microarray gene expression measures, in stage II colon cancer patients. Materials and Methods....
Colon Cancer Prognosis Prediction by Gene Expression Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Materials and Methods. Tumour (T)...
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on non-neoplastic mucosa microarray gene expression measures, in stage II colon cancer patients. Materials and Methods....
Colon Cancer Prognosis Prediction by Gene Expression Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Materials and Methods. Tumour (T)...
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (2005)
Barrier, Alain, Dudoit, Sandrine, Al., Et
Aims. This study assessed the possibility to build a prognosis predictor, based on non-neoplastic mucosa microarray gene expression measures, in stage II colon cancer patients. Materials and Methods....
Hothorn, Torsten, Buhlmann, Peter, Dudoit, Sandrine, Molinaro, Annette M., Van Der Laan, Mark J.
We propose a unified and flexible framework for ensemble learning in the presence of censoring. For right-censored data, we introduce a random forest algorithm and a generic gradient boosting...
Hothorn, Torsten, Buhlmann, Peter, Dudoit, Sandrine, Molinaro, Annette M., Van Der Laan, Mark J.
We propose a unified and flexible framework for ensemble learning in the presence of censoring. For right-censored data, we introduce a random forest algorithm and a generic gradient boosting...
Hothorn, Torsten, Buhlmann, Peter, Dudoit, Sandrine, Molinaro, Annette M., Van Der Laan, Mark J.
We propose a unified and flexible framework for ensemble learning in the presence of censoring. For right-censored data, we introduce a random forest algorithm and a generic gradient boosting...
Hothorn, Torsten, Buhlmann, Peter, Dudoit, Sandrine, Molinaro, Annette M., Van Der Laan, Mark J.
We propose a unified and flexible framework for ensemble learning in the presence of censoring. For right-censored data, we introduce a random forest algorithm and a generic gradient boosting...
Durbin, Blythe, Dudoit, Sandrine, Van Der Laan, Mark J.
Neural networks are a popular machine learning tool, particularly in applications such as the prediction of protein secondary structure. However, overfitting poses an obstacle to their effective use...
Durbin, Blythe, Dudoit, Sandrine, Van Der Laan, Mark J.
Neural networks are a popular machine learning tool, particularly in applications such as the prediction of protein secondary structure. However, overfitting poses an obstacle to their effective use...
Durbin, Blythe, Dudoit, Sandrine, Van Der Laan, Mark J.
Neural networks are a popular machine learning tool, particularly in applications such as the prediction of protein secondary structure. However, overfitting poses an obstacle to their effective use...
Durbin, Blythe, Dudoit, Sandrine, Van Der Laan, Mark J.
Neural networks are a popular machine learning tool, particularly in applications such as the prediction of protein secondary structure. However, overfitting poses an obstacle to their effective use...
Multiple Testing Procedures and Applications to Genomics (2005)
Birkner, Merrill D., Pollard, Katherine S., Van Der Laan, Mark J., Dudoit, Sandrine
This chapter proposes widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving...
Multiple Testing Procedures and Applications to Genomics (2005)
Birkner, Merrill D., Pollard, Katherine S., Van Der Laan, Mark J., Dudoit, Sandrine
This chapter proposes widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving...
Multiple Testing Procedures and Applications to Genomics (2005)
Birkner, Merrill D., Pollard, Katherine S., Van Der Laan, Mark J., Dudoit, Sandrine
This chapter proposes widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving...
Multiple Testing Procedures and Applications to Genomics (2005)
Birkner, Merrill D., Pollard, Katherine S., Van Der Laan, Mark J., Dudoit, Sandrine
This chapter proposes widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving...
Multiple Testing Procedures for Controlling Tail Probability Error Rates (2004)
Dudoit, Sandrine, Van Der Laan, Mark J., Birkner, Merrill D.
The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false...
Multiple Testing Procedures for Controlling Tail Probability Error Rates (2004)
Dudoit, Sandrine, Van Der Laan, Mark J., Birkner, Merrill D.
The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false...
Multiple Testing Procedures for Controlling Tail Probability Error Rates (2004)
Dudoit, Sandrine, Van Der Laan, Mark J., Birkner, Merrill D.
The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false...
Multiple Testing Procedures for Controlling Tail Probability Error Rates (2004)
Dudoit, Sandrine, Van Der Laan, Mark J., Birkner, Merrill D.
The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false...
Multiple Testing Procedures: R multtest Package and Applications to Genomics (2004)
Pollard, Katherine S., Dudoit, Sandrine, Van Der Laan, Mark J.
The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in...
Multiple Testing Procedures: R multtest Package and Applications to Genomics (2004)
Pollard, Katherine S., Dudoit, Sandrine, Van Der Laan, Mark J.
The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in...
Multiple Testing Procedures: R multtest Package and Applications to Genomics (2004)
Pollard, Katherine S., Dudoit, Sandrine, Van Der Laan, Mark J.
The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in...
Multiple Testing Procedures: R multtest Package and Applications to Genomics (2004)
Pollard, Katherine S., Dudoit, Sandrine, Van Der Laan, Mark J.
The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in...
Asymptotically optimal model selection method with right censored outcomes (2004)
Keles, Sündüz, Van Der Laan, Mark, Dudoit, Sandrine
Over the last two decades, nonparametric and semi-parametric approaches that adapt well-known techniques such as regression methods to the analysis of right censored data, e.g. right censored...
Bioconductor: open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C, Carey, Vincent J, Bates, Douglas M, Bolstad, Ben, Dettling, Marcel, Dudoit, Sandrine, ...
Abstract The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering...
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks (2004)
Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new...
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks (2004)
Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new...
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks (2004)
Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new...
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks (2004)
Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new...
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
This article shows that any single-step or stepwise multiple testing procedure (asymptotically) controlling the family-wise error rate (FWER) can be augmented into procedures that (asymptotically)...
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
This article shows that any single-step or stepwise multiple testing procedure (asymptotically) controlling the family-wise error rate (FWER) can be augmented into procedures that (asymptotically)...
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
This article shows that any single-step or stepwise multiple testing procedure (asymptotically) controlling the family-wise error rate (FWER) can be augmented into procedures that (asymptotically)...
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
This article shows that any single-step or stepwise multiple testing procedure (asymptotically) controlling the family-wise error rate (FWER) can be augmented into procedures that (asymptotically)...
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (2004)
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics...
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (2004)
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics...
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (2004)
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics...
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (2004)
Van Der Laan, Mark J., Dudoit, Sandrine, Pollard, Katherine S.
The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics...
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates (2004)
Dudoit, Sandrine, Van Der Laan, Mark J., Pollard, Katherine S.
The present article proposes general single-step multiple testing procedures for controlling Type I error rates defined as arbitrary parameters of the distribution of the number of Type I errors,...