Research Topics
| RAFAEL ANGEL IRIZARRYSummaryAffiliation: Johns Hopkins University Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Feature-level exploration of a published Affymetrix GeneChip control datasetRafael A Irizarry
Genome Biol 7:404. 2006..A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16...- Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarraysShin Lin
McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, N Broadway, Baltimore, MD 21205, USA
Genome Biol 9:R63. 2008..Also, we tie our call confidence metric to percent accuracy. We intend that our validation datasets and methods, refered to as SNPaffycomp, serve as standard benchmarks for future SNP calling algorithms... - Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequencesSrinivasan Yegnasubramanian
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
BMC Genomics 12:313. 2011..This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells... - Thawing Frozen Robust Multi-array Analysis (fRMA)Matthew N McCall
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
BMC Bioinformatics 12:369. 2011..Curation of such a database and creation of the frozen parameter estimates is time-consuming; therefore, fRMA has only been implemented on the most widely used Affymetrix platforms... - Assessing affymetrix GeneChip microarray qualityMatthew N McCall
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N, Wolfe St, Baltimore, MD, USA
BMC Bioinformatics 12:137. 2011.... - A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse databaseSimon Katz
Gene Logic Inc, 610 Professional Dr, Gaithersburg, MD, 20876, USA
BMC Bioinformatics 7:464. 2006..All subsequent pre-processing tasks can be done on an individual array basis. We demonstrate the utility of this approach by defining a new version of the Robust Multi-chip Averaging (RMA) algorithm which we refer to as refRMA... - Comparison of Affymetrix GeneChip expression measuresRafael A Irizarry
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA
Bioinformatics 22:789-94. 2006..A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted... - Comprehensive high-throughput arrays for relative methylation (CHARM)Rafael A Irizarry
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
Genome Res 18:780-90. 2008..Furthermore, unlike the other approaches, CHARM is highly quantitative, a substantial advantage in application to the study of human disease... - Multiple-laboratory comparison of microarray platformsRafael A Irizarry
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
Nat Methods 2:345-50. 2005..We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well... - Exploration, normalization, and summaries of high density oligonucleotide array probe level dataRafael A Irizarry
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
Biostatistics 4:249-64. 2003..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities... - Summaries of Affymetrix GeneChip probe level dataRafael A Irizarry
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
Nucleic Acids Res 31:e15. 2003..In particular, improvements in the ability to detect differentially expressed genes are demonstrated... - Assessing homeostasis through circadian patternsR A Irizarry
Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
Biometrics 57:1228-37. 2001..We then assess homeostasis using these estimates and their statistical properties...
Research Grants
- Analysis Tools and Software for Second Generation Sequencing DataRAFAEL ANGEL IRIZARRY; Fiscal Year: 2010..We will develop data analysis tools for widely used applications using statistical methods that account for this uncertainty. ..
- Software for the Statistical Analysis of Microarray Probe Level DataRafael Irizarry; Fiscal Year: 2007..Our proposed goal is to continue the support of our software and further develop our tools to increase their usefulness to the research community. ..
- Preprocessing and Analysis Tools for Contemporary Microarray ApplicationsRafael Irizarry; Fiscal Year: 2007....
- Software for the Statistical Analysis of Microarray Probe Level DataRafael Irizarry; Fiscal Year: 2009..Our proposed goal is to continue the support of our software and further develop our tools to increase their usefulness to the research community. ..
- Preprocessing and Analysis Tools for Contemporary Microarray ApplicationsRAFAEL ANGEL IRIZARRY; Fiscal Year: 2010..abstract_text> ..