title: Visualization and Differential Analysis of Protein Expression Data Using R.
abstract: Data analysis is essential to derive meaningful conclusions from proteomic data. This chapter describes ways of performing common data visualization and differential analysis tasks on gel-based proteomic datasets using a freely available statistical software package (R). A workflow followed is illustrated using a synthetic dataset as example.
authors.affiliation: SPAROS Lda., Área Empresarial de Marim, Lote C, 8700-221, Olhão, Portugal. tome@tomesilva.com.
authors.forename: Tomé S
authors.initials: TS
authors.lastname: Silva
authors.affiliation: CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
authors.forename: Nadège
authors.initials: N
authors.lastname: Richard
mesh_terms: D000465:Algorithms; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D020543:Proteome
keywords: Data visualization; Differential analysis; Feature selection; Heatmap; Hypothesis testing; Independent component analysis; Multidimensional scaling; Proteomics; R; Two-dimensional gel electrophoresis