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STAT540-UBC-2022 / project-team-11

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Final Proposal Feedback #2

Open asfarlathif opened 2 years ago

asfarlathif commented 2 years ago

HI Team 11,

Great proposal! Here are some of my feedback and thoughts on it:

  1. How is your initial DE analysis going to be different from the original study? What was the pipeline they used and how is your pipeline going to be different. It would also be nice to compare the DEG list they got with the set you obtain and explain the difference with the choice of tools you use
  2. In Q2 Are the significantly differentially expressed genes directly connected to immune response? you could do gene ontology enrichment on the obtained set of DEGs rather than manually comparing the immune related gene from DAVID with your set. Gene Ontology enrichment analysis are designed to find statistically enriched gene sets
  3. It is unclear wat your modelling variables in the ML part of the proposal. what's the rationale behind using PCA and on what basis do you think the patients are going to be clustered and into how many groups? are you going to use the PCs to predict on test set of patients?

Mark 5/5

YPARK commented 2 years ago

Good job, team 11. As for the third point that @asfarlathif raised, I hope forthcoming lectures can help provide sufficient background knowledge.