Supervised normalisation can bias microbiome analyses

Update 10/08/2023 Dr Sepich-Poore has raised some important points in an issue posted to GitHub here. I’d like to start by thanking Dr Sepich-Poore for highlighting these issues and providing constructive feedback. I also wish to emphasize that the analysis in my blog doesn’t definitively determine the presence or absence of a cancer-specific microbial signature in the TCGA data; rather, it emphasises the importance of normalisation in microbiome studies. The first important point raised by Dr Sepich-Poore, is that the use of Supervised Normalisation in the original TCGA paper did not include cancer type as the biological variable of interest.