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

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 .

Targeted Proteomics Approach for Precision Plant Breeding

“…20 The data were then normalized using the Loess regression method 24 (Loess-G) selected using Normalyzer. 25 …”

“…The data were then normalized using Loess regression 24 applied to replicates (Loess-R) using Normalyzer. 25 Arithmetic mean of the peptide intensity from replicates was used as a representative value for each clone in the segregating population.…”

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

“…The inadequate coverage of these methods may weaken the applicability range of those pipelines. Moreover, the suitability of a normalization method was reported to be greatly dependent on the nature of the analyzed data53, a comparative performance evaluation among methods is therefore essential to the determination of the most appropriate method for professional/inexperienced researchers. However, no comparative evaluation among those normalization methods was conducted in the above pipelines.…”

“…However, no comparative evaluation among those normalization methods was conducted in the above pipelines. So far, the Normalyzer 53 is the only online tool offering comparative evaluation of 12 different normalization methods treating high-throughput OMICs data53. In particular, this tool accepted a variety of data types including metabolomics, proteomics, DNA microarray and the real-time polymerase chain reaction data53.…”

“…So far, the Normalyzer 53 is the only online tool offering comparative evaluation of 12 different normalization methods treating high-throughput OMICs data53. In particular, this tool accepted a variety of data types including metabolomics, proteomics, DNA microarray and the real-time polymerase chain reaction data53. However, since the Normalyzer was designed to process a wide range of OMICs, it did not cover 8 of those 16 methods specifically for LC/MS based metabolomics studies.…”