Apr 29, 2014

Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets

Journal of Proteome Research
Aakash ChawadeFredrik Levander

Abstract

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 .

  • References11
  • Citations55

Citations

Mentioned in this Paper

Tandem Mass Spectrometry
Computer Programs and Programming
Proteomics
Proteome
Data Interpretation, Statistical
Cdna Microarrays
MRNA Differential Display

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