Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies.
Microbiome data obtained with amplicon sequencing are considered as compositional data. It has been argued that these data can be analysed after appropriate transformation to log-ratios, but ratios and logarithms cause problems with the many zeroes in typical microbiome experiments. We demonstrate t...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0292055&type=printable |
| _version_ | 1797666846100422656 |
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| author | Leyla Kodalci Olivier Thas |
| author_facet | Leyla Kodalci Olivier Thas |
| author_sort | Leyla Kodalci |
| collection | DOAJ |
| description | Microbiome data obtained with amplicon sequencing are considered as compositional data. It has been argued that these data can be analysed after appropriate transformation to log-ratios, but ratios and logarithms cause problems with the many zeroes in typical microbiome experiments. We demonstrate that some well chosen sign and rank transformations also allow for valid inference with compositional data, and we show how logistic regression and probabilistic index models can be used for testing for differential abundance, while inheriting the flexibility of a statistical modelling framework. The results of a simulation study demonstrate that the new methods perform better than most other methods, and that it is comparable with ANCOM-BC. These methods are implemented in an R-package 'signtrans' and can be installed from Github (https://github.com/lucp9827/signtrans). |
| first_indexed | 2024-03-11T20:04:28Z |
| format | Article |
| id | doaj.art-71097304c8604d4188129d0942160f52 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-11T20:04:28Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-71097304c8604d4188129d0942160f522023-10-04T05:31:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01189e029205510.1371/journal.pone.0292055Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies.Leyla KodalciOlivier ThasMicrobiome data obtained with amplicon sequencing are considered as compositional data. It has been argued that these data can be analysed after appropriate transformation to log-ratios, but ratios and logarithms cause problems with the many zeroes in typical microbiome experiments. We demonstrate that some well chosen sign and rank transformations also allow for valid inference with compositional data, and we show how logistic regression and probabilistic index models can be used for testing for differential abundance, while inheriting the flexibility of a statistical modelling framework. The results of a simulation study demonstrate that the new methods perform better than most other methods, and that it is comparable with ANCOM-BC. These methods are implemented in an R-package 'signtrans' and can be installed from Github (https://github.com/lucp9827/signtrans).https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0292055&type=printable |
| spellingShingle | Leyla Kodalci Olivier Thas Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. PLoS ONE |
| title | Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. |
| title_full | Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. |
| title_fullStr | Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. |
| title_full_unstemmed | Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. |
| title_short | Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies. |
| title_sort | simple and flexible sign and rank based methods for testing for differential abundance in microbiome studies |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0292055&type=printable |
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