Preface

#> working directory clean

This manuscript was rendered from commit 414f6e78cc9b29c8236c8c3e996b68cd4d733b86.

This in-progress manuscript is not intended for general scientific use. It is incomplete, has not been carefully reviewed, and may contain mistakes or other inaccuracies. Please post comments or questions on the GitHub Issues page or email Mike.

This manuscript addresses the effect that the taxonomic bias inherent in microbiome measurement has on microbial differential-abundance analysis. We describe the basic problem posed by taxonomic bias for measuring changes in the abundance of particular taxa across conditions and describe new strategies for mitigating the errors it induces. Analyses of both relative and absolute abundances are considered. In its current form, the manuscript sits somewhere between a standard scientific article and a monograph; it consists of an article followed by a series of appendices which together give a comprehensive treatment of the implications of the McLaren, Willis, and Callahan (2019) model of taxonomic bias for differential-abundance analysis and experimental design. It is licensed under a CC BY 4.0 License. See the Zenodo record for how to cite the latest version.

References

McLaren, Michael R, Amy D Willis, and Benjamin J Callahan. 2019. “Consistent and correctable bias in metagenomic sequencing experiments.” Elife 8 (September): 46923. https://doi.org/10.7554/eLife.46923.

  1. North Carolina State University; send correspondence to ↩︎

  2. Dalhousie University↩︎

  3. University of Washington↩︎

  4. University of Tennessee↩︎

  5. North Carolina State University↩︎