Work

The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance

Year: 2018

Type: conference-paper

Abstract: Three common methods, normalization, log transformation, and rarefaction, for handling outliers and erroneous abundances in Operational Taxonomic Unit (OTU) tables are tested for effects in K-means and PCA clustering as well as effects in NMF. We find that of the three methods, log transformation is closest to the unmodified OTUs data, also indicating that when doing specific types of clustering analysis on OTU data, if outliers are to be adjusted within a clustering analysis, a log transformation may be applied.

Source: IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI: 10.1109/bibm.2018.8621347

Authors: DeAndre A. Tomlinson, David C. Molik, Michael E. Pfrender, Scott J. Emrich

Institutions: University of Notre Dame, University of Tennessee at Knoxville

Language: English

Topic: Microbial Community Ecology and Physiology

Subfield: Ecology

Field: Environmental Science

Domain: Physical Sciences

Open Access status: green

OpenAlex ID: W2950536358

FWCI: 1.311

Cites: 10

Cited by: 2

Related to: 10