A framework for oligonucleotide microarray preprocessing
Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existi...
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| Published in | Bioinformatics Vol. 26; no. 19; pp. 2363 - 2367 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
01.10.2010
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btq431 |
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| Abstract | Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages. Availability: The oligo package is freely available through BioConductor, http://www.bioconductor.org. Contact: benilton.carvalho@cancer.org.uk; rafa@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
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| AbstractList | Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools.Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages. The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages. The oligo package is freely available through BioConductor, http://www.bioconductor.org. The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools.MOTIVATIONThe availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools.We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages.RESULTSWe developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages.The oligo package is freely available through BioConductor, http://www.bioconductor.org.AVAILABILITYThe oligo package is freely available through BioConductor, http://www.bioconductor.org. Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages. Availability: The oligo package is freely available through BioConductor, http://www.bioconductor.org. Contact: benilton.carvalho@cancer.org.uk; rafa@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages. Availability: The oligo package is freely available through BioConductor, http://www.bioconductor.org. Contact: benilton.carvalho@cancer.org.uk; rafa@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
| Author | Carvalho, Benilton S. Irizarry, Rafael A. |
| AuthorAffiliation | 1 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and 2 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA |
| AuthorAffiliation_xml | – name: 1 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and 2 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA |
| Author_xml | – sequence: 1 givenname: Benilton S. surname: Carvalho fullname: Carvalho, Benilton S. organization: Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA – sequence: 2 givenname: Rafael A. surname: Irizarry fullname: Irizarry, Rafael A. organization: Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23272902$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/20688976$$D View this record in MEDLINE/PubMed |
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| Keywords | Microarray Oligonucleotide DNA chip |
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| References | Carvalho (2023012508170251300_B2) 2007; 8 Clark (2023012508170251300_B4) 2007; 8 Carvalho (2023012508170251300_B3) 2010; 26 Ritchie (2023012508170251300_B13) 2009; 25 Gitan (2023012508170251300_B7) 2002; 12 Irizarry (2023012508170251300_B8) 2008; 18 Irizarry (2023012508170251300_B11) 2006; 22 Bolstad (2023012508170251300_B1) 2003; 19 Gentleman (2023012508170251300_B6) 2004; 5 Irizarry (2023012508170251300_B10) 2003; 2 The International HapMap Consortium (2023012508170251300_B15) 2003; 426 Irizarry (2023012508170251300_B9) 2003; 4 Irizarry (2023012508170251300_B12) 2006; 7 Scharpf (2023012508170251300_B14) 2008; 2 Gautier (2023012508170251300_B5) 2004; 20 |
| References_xml | – volume: 2 start-page: 687 year: 2008 ident: 2023012508170251300_B14 article-title: Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays publication-title: Ann. Appl. Stat. doi: 10.1214/07-AOAS155 – volume: 426 start-page: 789 year: 2003 ident: 2023012508170251300_B15 article-title: The International HapMap Project publication-title: Nature doi: 10.1038/nature02168 – volume: 8 start-page: 485 year: 2007 ident: 2023012508170251300_B2 article-title: Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data publication-title: Biostatistics doi: 10.1093/biostatistics/kxl042 – volume: 5 start-page: R80 year: 2004 ident: 2023012508170251300_B6 article-title: Bioconductor: open software development for computational biology and bioinformatics publication-title: Genome Biol. doi: 10.1186/gb-2004-5-10-r80 – volume: 25 start-page: 2621 year: 2009 ident: 2023012508170251300_B13 article-title: R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp470 – volume: 26 start-page: 242 year: 2010 ident: 2023012508170251300_B3 article-title: Quantifying uncertainty in genotype calls publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp624 – volume: 8 start-page: R64 year: 2007 ident: 2023012508170251300_B4 article-title: Discovery of tissue-specific exons using comprehensive human exon microarrays publication-title: Genome Biol. doi: 10.1186/gb-2007-8-4-r64 – volume: 4 start-page: 249 year: 2003 ident: 2023012508170251300_B9 article-title: Exploration, normalization, and summaries of high density oligonucleotide array probe level data publication-title: Biostatistics doi: 10.1093/biostatistics/4.2.249 – volume: 20 start-page: 307 year: 2004 ident: 2023012508170251300_B5 article-title: affy—analysis of affymetrix genechip data at the probe level publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg405 – volume: 19 start-page: 185 year: 2003 ident: 2023012508170251300_B1 article-title: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias publication-title: Bioinformatics doi: 10.1093/bioinformatics/19.2.185 – volume: 18 start-page: 780 year: 2008 ident: 2023012508170251300_B8 article-title: Comprehensive high-throughput arrays for relative methylation (CHARM) publication-title: Genome Res. doi: 10.1101/gr.7301508 – volume: 12 start-page: 158 year: 2002 ident: 2023012508170251300_B7 article-title: Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis publication-title: Genome Res. doi: 10.1101/gr.202801 – volume: 2 year: 2003 ident: 2023012508170251300_B10 article-title: Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants publication-title: Stat. Appl. Genet. Mol. Biol. doi: 10.2202/1544-6115.1002 – volume: 22 start-page: 789 year: 2006 ident: 2023012508170251300_B11 article-title: Comparison of affymetrix genechip expression measures publication-title: Bioinformatics doi: 10.1093/bioinformatics/btk046 – volume: 7 start-page: 404 year: 2006 ident: 2023012508170251300_B12 article-title: Feature-level exploration of a published affymetrix genechip control dataset publication-title: Genome Biol. doi: 10.1186/gb-2006-7-8-404 |
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| SubjectTerms | Algorithms Biological and medical sciences Databases, Factual Fundamental and applied biological sciences. Psychology Gene Expression Profiling - methods General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Oligonucleotide Array Sequence Analysis - methods Oligonucleotides Original Papers Software User-Computer Interface |
| Title | A framework for oligonucleotide microarray preprocessing |
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