title: Comparison of pre-processing methods for multiplex bead-based immunoassays.
abstract: BACKGROUND
  High throughput protein expression studies can be performed using bead-based protein immunoassays, such as the Luminex® xMAP® technology. Technical variability is inherent to these experiments and may lead to systematic bias and reduced power. To reduce technical variability, data pre-processing is performed. However, no recommendations exist for the pre-processing of Luminex® xMAP® data.
  
  
  RESULTS
  We compared 37 different data pre-processing combinations of transformation and normalization methods in 42 samples on 384 analytes obtained from a multiplex immunoassay based on the Luminex® xMAP® technology. We evaluated the performance of each pre-processing approach with 6 different performance criteria. Three performance criteria were plots. All plots were evaluated by 15 independent and blinded readers. Four different combinations of transformation and normalization methods performed well as pre-processing procedure for this bead-based protein immunoassay.
  
  
  CONCLUSIONS
  The following combinations of transformation and normalization were suitable for pre-processing Luminex® xMAP® data in this study: weighted Box-Cox followed by quantile or robust spline normalization (rsn), asinh transformation followed by loess normalization and Box-Cox followed by rsn.
authors: Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
authors: Tanja K
authors: TK
authors: Rausch
authors: Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
authors: Arne
authors: A
authors: Schillert
authors: Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany. ziegler@imbs.uni-luebeck.de.|Zentrum für Klinische Studien, Universität zu Lübeck, Lübeck, Germany. ziegler@imbs.uni-luebeck.de.|School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa. ziegler@imbs.uni-luebeck.de.
authors: Andreas
authors: A
authors: Ziegler
authors: Protagen AG, Dortmund, Germany.
authors: Angelika
authors: A
authors: Lüking
authors: Protagen AG, Dortmund, Germany.
authors: Hans-Dieter
authors: HD
authors: Zucht
authors: Protagen AG, Dortmund, Germany. peter.schulz-knappe@protagen.com.
authors: Peter
authors: P
authors: Schulz-Knappe
mesh_terms: D001323:Autoantibodies / Q000097:blood* / Q000235:genetics; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data*; D005786:Gene Expression Regulation; D006801:Humans; D007118:Immunoassay / Q000592:standards* / Q000706:statistics & numerical data; D008163:Luminescent Measurements; D009103:Multiple Sclerosis / Q000097:blood / Q000276:immunology / Q000473:pathology; D009471:Neuromyelitis Optica / Q000097:blood / Q000276:immunology / Q000473:pathology; D015588:Observer Variation; D015203:Reproducibility of Results
chemical_list: D001323:Autoantibodies
keywords: Autoantibody; Bead-based; Immunoassay; Luminex; Multiplex; Omics; Pre-processing; Protein