A study published in GenomeMedicine suggests that profiling of bacterial composition can be developed into a stratification biomarker for prognosis predictions and implementation of colon cancer therapies.
To correct for the identified batch effect, the reconstructed bacterial microbiome relative abundances were scaled and log-transformed. After that, we applied the ComBat function from the sva package in R [], controlling for the known batch covariate . Since some cancer types have few samples per plate, we pooled the plates with a low number of samples: plates were pooled if they had less than 10% of the total number of samples , if frac > 5, frac was set to 5.
Tumour property association with microbiome composition: to test the specific association between the PCs and the tumour properties, we ran the PCA and compared the different distributions of the PC coordinates with the subgroups we were analysing with the Wilcoxon or Kruskal–Wallis test. We also tested the correlation between PC coordinates and the tumour properties values with the Spearman correlation test.
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