Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets

Research output: Contribution to journalArticle


High-throughput omics data often contain systematic biases introduced during various steps of sample processing and data generation. As the source of these biases is usually unknown, it is difficult to select an optimal normalization method for a given data set. To facilitate this process, we introduce the open-source tool "Normalyzer". It normalizes the data with 12 different normalization methods and generates a report with several quantitative and qualitative plots for comparative evaluation of different methods. The usefulness of Normalyzer is demonstrated with three different case studies from quantitative proteomics and transcriptomics. The results from these case studies show that the choice of normalization method strongly influences the outcome of downstream quantitative comparisons. Normalyzer is an R package and can be used locally or through the online implementation at


Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Immunology in the medical area


  • normalization, preprocessing, label-free, mass spectrometry, microarray, proteomics, transcriptomics
Original languageEnglish
Pages (from-to)3114-3120
JournalJournal of Proteome Research
Issue number6
Publication statusPublished - 2014
Publication categoryResearch