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

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Author

Summary, in English

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 http://quantitativeproteomics.org/normalyzer.

Publishing year

2014

Language

English

Pages

3114-3120

Publication/Series

Journal of Proteome Research

Volume

13

Issue

6

Document type

Journal article

Publisher

The American Chemical Society (ACS)

Topic

  • Immunology in the medical area

Keywords

  • normalization
  • preprocessing
  • label-free
  • mass spectrometry
  • microarray
  • proteomics
  • transcriptomics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1535-3893