Chapter 14 Lab 1

14.1 unsupervised learning: Feature selection & dimension reduction

  1. Make the tse (TreeSummarizedExperiment) Object for the further analysis (use the provided script to make a tse )

14.2 Load the data

  1. Aggregate the data to Phylum level (agglomerateByRank)

  2. Subset the data at the Species level with only taking bacterial Species that are greater than 10% of prevalence in the total sample

  3. Subset a tse object which consist only two phyla i.e Actinobacteria”, “Cyanobacteria

  4. Calculate relative abundances, and store the table to assays

6.Perform a centred log-ratio transformation (clr) (i.e. mia::transformSamples)