poster

The UniFrac significance test generates different outputs given semantically equivalent inputs

Authors:

Jeffrey Long,

Qingxiang Yan,

Brett Trost,

Anthony KusalikAuthors Info & Claims

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Page 589

https://doi.org/10.1145/2649387.2660784

Published: 20 September 2014 Publication History

Abstract

UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities in meta-genomic studies. We identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.

The phylogenetic trees that are input into UniFrac may or may not contain abundance counts. An isomorphic transform can be defined that will convert trees between these two formats without altering the semantic meaning of the trees. UniFrac produces different outputs for these equivalent forms of the same input tree. This is illustrated using metagenomics data from a lake sediment study. Practitioners should be aware of this issue and use the tool with caution to ensure consistency and validity in their analyses.

Index Terms

The UniFrac significance test generates different outputs given semantically equivalent inputs
1. Applied computing
  1. Life and medical sciences
  2. Physical sciences and engineering
    1. Mathematics and statistics
2. Mathematics of computing
  1. Discrete mathematics
  2. Mathematical software
    1. Statistical software

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Information & Contributors

Information

Published In

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

September 2014

851 pages

ISBN:9781450328944

DOI:10.1145/2649387

General Chairs:
Pierre Baldi
University of California, Irvine
,
Wei Wang
University of California, Los Angeles

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 20 September 2014

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Author Tags

Qualifiers

Poster

Conference

BCB '14

Sponsor:

SIGBio

BCB '14: ACM-BCB '14

September 20 - 23, 2014

California, Newport Beach

Acceptance Rates

Overall Acceptance Rate 254 of 885 submissions, 29%

Index Terms

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