title: RPPanalyzer toolbox: an improved R package for analysis of reverse phase protein array data.
abstract: Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce an extension of an open-source software solution for analyzing reverse phase protein array (RPPA) data. The R package RPPanalyzer was designed for data preprocessing followed by basic statistical analyses and proteomic data visualization. In this update, we merged relevant data preprocessing steps into a single user-friendly function and included a new method for background noise correction as well as new methods for noise estimation and averaging of replicates to transform data in such a way that they can be used as input for a new time course plotting function. We demonstrate the robustness of our enhanced RPPanalyzer platform by analyzing longitudinal RPPA data of MET receptor signaling upon stimulation with different hepatocyte growth factor concentrations.
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Silvia
authors.initials: S
authors.lastname: von der Heyde
authors.affiliation: Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Johanna
authors.initials: J
authors.lastname: Sonntag
authors.affiliation: Institute of Physics, Freiburg University, Freiburg, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Kaschek
authors.affiliation: TRON-Translational Oncology at the Johannes Gutenberg University of Mainz Medicine, Mainz, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Bender
authors.affiliation: Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Bues
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Astrid
authors.initials: A
authors.lastname: Wachter
authors.affiliation: Institute of Physics, Freiburg University, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Freiburg University, Freiburg, Germany; Freiburg Center for Systems Biology (ZBSA), Freiburg University, Freiburg, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Timmer
authors.affiliation: Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Korf
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Beißbarth
mesh_terms: D007091:Image Processing, Computer-Assisted / Q000379:methods*; D040081:Protein Array Analysis / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012984:Software
keywords: RPPA; RPPanalyzer; data analysis toolbox; open-source software; proteomics