Compositional transformations can reasonably introduce phenotype-associated values into sparse features.

Abstract excerpt

Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction. Here, we examine whether...

Topics

• Humans
• Phenotype
• Microbiota
• Female
• Machine Learning