A protocol to evaluate RNA sequencing normalization methods

Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R.O. Payne, Kevin Coombes

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Background: RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization. Results: In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested. Conclusion: Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.

Original languageEnglish
Article number679
JournalBMC bioinformatics
Volume20
DOIs
StatePublished - Dec 20 2019

Keywords

  • Biological variability
  • Normalization
  • RNASeq
  • Standardization

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