MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
Tóm tắt
We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA.
Tài liệu tham khảo
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
The Bioconductor Project. [http://www.bioconductor.org]
Ihaka R, Gentleman RC: R: a language for data analysis and graphics. J Computational Graphical Stat. 1996, 5: 299-314. 10.2307/1390807.
The R Project for Statistical Computing. [http://www.r-project.org]
Dalgaard P: The R-Tcl/Tk interface. Proceedings of the Second International Workshop on Distributed Statistical Computing: 15-17. Edited by: Hornik K, Leisch F. 2001, [http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/Dalgaard.pdf]March ; Vienna, Austria.
Fox J: The R commander: a basic-statistics graphical user interface to R. J Stat Software. 2005, 14: [http://www.jstatsoft.org/v14/i09/paper]
Grosjean P: SciViews: an object-oriented abstraction layer to design GUIs on top of various calculation kernels. Proceedings of the Third International Workshop on Distributed Statistical Computing: 20-22. Edited by: Hornik K, Leisch F, Zeileis A. 2003, [http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/Grosjean.pdf]March ; Vienna, Austria.
Wettenhall JM, Smyth GK: limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics. 2004, 20: 3705-3706. 10.1093/bioinformatics/bth449.
Wettenhall JM, Simpson KM, Satterley K, Smyth GK: affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics. 2006, 22: 897-899. 10.1093/bioinformatics/btl025.
Futschik ME, Crompton T: OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics. 2005, 21: 1724-1726. 10.1093/bioinformatics/bti199.
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J: TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003, 34: 374-378.
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863.
Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol. 2003, 4: R70-10.1186/gb-2003-4-10-r70.
SourceForge.net. [http://www.sourceforge.net/projects/mev-tm4]
Gottardo R, Raftery AE, Yeung KY, Bumgarner RE: Quality control and robust estimation for cDNA microarrays with replicates. J Am Stat Assoc. 2006, 101: 30-40. 10.1198/016214505000001096.
Gottardo R, Raftery AE, Yeung KY, Bumgarner RE: Bayesian robust inference for differential gene expression in cDNA microarrays with multiple samples. Biometrics. 2006, 62: 10-18. 10.1111/j.1541-0420.2005.00397.x.
Yeung KY, Bumgarner RE, Raftery AE: Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics. 2005, 21: 2394-2402. 10.1093/bioinformatics/bti319.
MeV+R Supplementary Web Site. [http://expression.washington.edu/mevr]
Urbanek S: Rserve - a fast way to provide R functionality to applications. Proceedings of the Third International Workshop on Distributed Statistical Computing: 20-22. Edited by: Hornik K, Leisch F, Zeileis A. 2003, [http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/Urbanek.pdf]March ; Vienna, Austria.
Rserve. [http://stats.math.uni-augsburg.de/Rserve]
MeV Manual. [http://www.tm4.org/mev.html]
Raftery AE: Bayesian model selection in social research (with discussion). Sociol Methodol. 1995, 25: 111-196. 10.2307/271063.
Dudoit S, Fridlyand J, Speed TP: Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc. 2002, 97: 77-87. 10.1198/016214502753479248.
van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI: Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. J Virol. 2003, 77: 1392-1402. 10.1128/JVI.77.2.1392-1402.2003.
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498.
Affymetrix U133 Spike-in Data. [http://www.affymetrix.com/support/technical/sample_data/datasets.affx]
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31: e15-10.1093/nar/gng015.
Sheffler W, Upfal E, Sedivy J, Noble WS: A learned comparative expression measure for affymetrix genechip DNA microarrays. Proc IEEE Comput Syst Bioinform Conf. 2005, 144-154.
Lo K, Gottardo R: Flexible empirical Bayes models for differential gene expression. Bioinformatics. 2007, 23: 328-335. 10.1093/bioinformatics/btl612.
Theilhaber J, Connolly T, Roman-Roman S, Bushnell S, Jackson A, Call K, Garcia T, Baron R: Finding genes in the C2C12 osteogenic pathway by k-nearest-neighbor classification of expression data. Genome Res. 2002, 12: 165-176. 10.1101/gr.182601.
Yeung KY, Bumgarner RE: Multiclass classification of microarray data with repeated measurements: application to cancer. Genome Biol. 2003, 4: R83-10.1186/gb-2003-4-12-r83.
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999, 286: 531-537. 10.1126/science.286.5439.531.
van 't Veer LJ, Dai H, Vijver van de MJ, He YD, Hart AA, Mao M, Peterse HL, Kooy van der K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002, 415: 530-536. 10.1038/415530a.
Pavlidis P, Noble WS: Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2001, 2: research0042.1-0042.15. 10.1186/gb-2001-2-10-research0042.