Abstract
In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R.
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References
Complete Blood Count, http://www.labtestsonline.org/understanding/analytes/cbc/test.html (last accessed October 2, 2012)
Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo (last accessed October 2, 2012)
R Documentation: Levelplot, http://stat.ethz.ch/R-manual/R-devel/library/lattice/html/levelplot.html (last accessed October 2, 2012)
R-project, http://www.r-project.org (last accessed October 2, 2012)
Scatterplot, http://www.stat.yale.edu/Courses/1997-98/101/scatter.htm (last accessed October 2, 2012)
SYSTHER project, http://systher.biologie.hu-berlin.de (last accessed October 2, 2012)
Blaese, L.: Data Mining for Unidentified Protein Sequences. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 73–87. Springer, Heidelberg (2014)
Cahan, P., Rovegno, F., Mooney, D., Newman, J.C., Laurent III, S., McCaffrey, T.A., McCaffrey, T.A.: Meta-Analysis of Microarray Results: Challenges, Opportunities, and Recommendations for Standardization, NIH-PA Author Manuscript (2007)
Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: Automating Metabolic Flux Analysis. Metabolites 2(4), 872–890 (2012)
Gruden, K., Hren, M., Herman, A., Blejec, A., Albrecht, T., Selbig, J., Bauer, C., Schuchardt, J., Or-Guil, M., Zupani, K., Svajger, U., Tabuc, B., Ihan, A., Kopitar, A., Ravnikar, M., Knezevic, M., Rozman, P., Jeras, M.: Large scale omics assessment of physiological variation in constituents of human blood periodically taken from a group of healthy volunteers (in preparation)
Huzarewich, R.L.C.H., Siemens, C.G., Both, S.A.: Application of omics to Prion Biomarker Discovery. Journal of Biomedicine and Biotechnology (2010)
Lamprecht, A.-L.: User-Level Workflow Design. LNCS, vol. 8311, pp. 1–202. Springer, Heidelberg (2013)
Lamprecht, A.-L., Margaria, T.: Scientific Workflows and XMDD. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 1–13. Springer, Heidelberg (2014)
Lamprecht, A.-L., Margaria, T., Steffen, B.: Seven variations of an alignment workflow - an illustration of agile process design and management in bio-jETI. In: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 445–456. Springer, Heidelberg (2008)
Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: a framework for semantics-based service composition. BMC Bioinformatics 10(Suppl 10), S8 (2009)
Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics 9(Suppl 4), S13 (2008)
Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. Journal of Biomedical Semantics 2(Suppl 1), S5 (2011)
Lamprecht, A.-L., Wickert, A.: The Course’s SIB Libraries. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 30–44. Springer, Heidelberg (2014)
Lis, M.: Constructing a Phylogenetic Tree. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 101–109. Springer, Heidelberg (2014)
Margaria, T., Steffen, B.: Agile IT: Thinking in User-Centric Models. In: Margaria, T., Steffen, B. (eds.) Leveraging Applications of Formal Methods, Verification and Validation. CCIS, vol. 17, pp. 490–502. Springer, Heidelberg (2009)
Margaria, T., Steffen, B.: Business Process Modelling in the jABC: The One-Thing-Approach. In: Cardoso, J., van der Aalst, W. (eds.) Handbook of Research on Business Process Modeling, IGI Global (2009)
Margaria, T., Steffen, B.: Continuous Model-Driven Engineering. IEEE Computer 42(10), 106–109 (2009)
Margaria, T., Steffen, B.: Simplicity as a Driver for Agile Innovation. Computer 43(6), 90–92 (2010)
Margaria, T., Steffen, B.: Service-Orientation: Conquering Complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, Heidelberg (2012)
Margaria, T., Steffen, B., Reitenspiess, M.: Service-oriented design: The roots. In: Benatallah, B., Casati, F., Traverso, P. (eds.) ICSOC 2005. LNCS, vol. 3826, pp. 450–464. Springer, Heidelberg (2005)
Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose Programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) Fundamental Approaches to Software Engineering. LNCS, vol. 7212, pp. 94–98. Springer, Heidelberg (2012)
Reso, J.: Protein Classification Workflow. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 65–72. Springer, Heidelberg (2014)
Schulze, G.: Workflow for Rapid Metagenome Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 88–100. Springer, Heidelberg (2014)
Schütt, C.: Identification of Differentially Expressed Genes. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 127–139. Springer, Heidelberg (2014)
Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-driven development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, pp. 92–108. Springer, Heidelberg (2007)
Swan, D.: Analysing micorarray data in Bioconductor, http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor (last accessed October 2, 2012)
Trevor Hastie, R.T., Friedman, J.: The elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd edn. Springer (2009)
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Vierheller, J. (2014). Exploratory Data Analysis. In: Lamprecht, AL., Margaria, T. (eds) Process Design for Natural Scientists. Communications in Computer and Information Science, vol 500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45006-2_9
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DOI: https://doi.org/10.1007/978-3-662-45006-2_9
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