Empirical Bayesian models for analysing molecular serotyping microarrays

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Newton, Richard ^a   Hinds, Jason ^b   Wernisch, Lorenz ^a  

^a MRC BIOSTATISTICS UNIT   (United Kingdom)

^b ST GEORGE'S UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSULAR POLYSACCHARIDES; EMPIRICAL BAYESIAN; INFECTIOUS DISEASE; MOLECULAR DIAGNOSTICS; OLIGONUCLEOTIDE PROBES; RANDOM EFFECTS MODEL; RELATIVE ABUNDANCE; STREPTOCOCCUS PNEUMONIAE;

BAYESIAN NETWORKS; GENES; OLIGONUCLEOTIDES; PROBES;

MICROARRAYS;

STREPTOCOCCUS PNEUMONIAE;

ARTICLE; BACTERIUM IDENTIFICATION; BAYES THEOREM; CLASSIFICATION; DNA MICROARRAY; GENETICS; METHODOLOGY; PROBABILITY; REPRODUCIBILITY; SEROTYPING; STREPTOCOCCUS PNEUMONIAE;

BACTERIAL TYPING TECHNIQUES; BAYES THEOREM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROBABILITY; REPRODUCIBILITY OF RESULTS; SEROTYPING; STREPTOCOCCUS PNEUMONIAE;

EID: 79953214614     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-88     Document Type: Article

References (16)

1. Boriskin YS, Rice PS, Stabler RA, Hinds J, Al-Ghusein H, Vass K, Butcher PD. DNA Microarrays for Virus Detection in cases of Central Nervous System Infection. Journal of Clinical Microbiology 2004, 42:5811-5818. 10.1128/JCM.42.12.5811-5818.2004, 535236, 15583316.
2. Loy A, Bodrossy L. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clinica Chimica Acta 2006, 363:106-119.
3. Stabler RA, Dawson LF, Oyston PC, Titball RW, Wade J, Hinds J, Witney A, Wren BW. Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux. BMC Microbiology 2008, 8:177. 10.1186/1471-2180-8-177, 2607285, 18844996.
4. Hinds J, Gould KA, Witney AA, Baldry SJ, Lambertsen L, Hannage WP, Antonio M, Turner P, Newton R, Wernisch L, Aanensen DM, Bentley S. Molecular serotyping of Streptococcus pneumoniae: a microarray-based tool with enhanced utility for isolate typing, novel serotype discovery, non-typeable investigation, multiple carriage detection, and direct analysis of nasopharyngeal swabs [Abstract A-O5]. 9th European Meeting on the Molecular Biology of the Pneumococcus (Europneumo). Bern, Switzerland 2009,
5. Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbi-nowitsch E, Collins M, Donohoe K, Harris D, Murphy L, Quail MA, Samuel G, Skovsted IC, Kaltoft MS, Barrell B, Reeves PR, Parkhill J, Spratt BG. Genetic analysis of the capsular biosyn-thetic locus from all 90 pneumococcal serotypes. PLOS Genetics 2006, 2:262-269.
6. Aanensen DM, Mavroidi A, Bentley SD, Reeves PR, Spratt BG. Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol 2007, 189(21):7856-7876. 10.1128/JB.00837-07, 2168755, 17766420.
7. Mavroidi A, Aanensen DM, Godo Y, Skovsted IC, Kaltoft MS, Reeves PR, Bentley SD, Spratt BG. Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacte-riol 2007, 189(21):7841-7855.
8. Agilent. , http://www.agilent.com
9. Park IH, Park S, Hollingshead SK, Nahm MH. Genetic basis for the new pneumococcal serotype 6C. Infection and Immunity 2007, 75:4482-4489. 10.1128/IAI.00510-07, 1951153, 17576753.
10. Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
11. R Development Core Team R: A language and environment for statistical computing 2004, R Foundation for Statistical Computing, Vienna, Austria, [3-900051-07-0], R Development Core Team., http://www.R-project.org
12. Lindsey J. Utilities for Nonlinear Regression and Repeated Measurements Models. , http://www.commanster.eu/rcode.html
13. Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, A H, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, J PM. TRANSBIG Consortium. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006, 98(17):1183-1192. 10.1093/jnci/djj329, 16954471.
14. Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, Firth H, Sanlaville D, Winter R, Colleaux L, Bobrow M, Carter NP. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004, 41(4):241-248. 10.1136/jmg.2003.017731, 1735726, 15060094.
15. Blangiardo M, Toti1 S, Giusti B, Abbate R, Magi A, Poggi F, Rossi L, Torricelli F, Biggeri A. Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data. Bioinformatics 2006, 22(1):50-57. 10.1093/bioinformatics/bti750, 16267084.
16. Newton R, Wernisch L. Rwui: A web application to create user friendly web interfaces for R scripts. R News 2007, 7(2):32-35.