Feature-selection microbiome data to build a model to predict cancer

Question

I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples).

I have filtered the data using filtering approach by Duvallet(removing samples with fewer than 100 reads and OTUs with fewer than 10 reads,as well as OTUs which were present in fewer than 1% within the study) What do I have to do after the preprocessing step? How can I do the feature selection for the phenotype data and the microbiome data?

Answer 1

I think the question needs improving. As the question stands pre-processing to feature selection ML (that's whats being asked).

• put the species diversity into a pandas dataframe the last column is the target (cancer vs healthy).
• assess a variety of ML algorithms (because they give different answers). Naive bayes, linear regression and K-nearest neighbour (KNN) are simple algorithms, easy to run and at this level fine.
• each have a "feature selection" - all features will be positive.

At a personal level I like KNN, but avoid LR and NB.

I personally would simply suggest unsupervised learning.