CSC483 HW06

CSC 483: Homework 6, Due Feb 17, 2026, at 1 pm

1. Project Proposal (2 pts + 2pts in PR)

  1. Continue working in your notebook from last week, adding any exploratory analyses you do to come up with a question to answer for your project.

  2. Inlcude what data you will use to answer your question and what fields you will focus on.

  3. Specify how you will filter your data to be able to answer your question without loading unnecesary data.

  4. Specify which dimentionailty reduction method(s) you would like to use. These can be any flavor of PCA or embeddings like t-SNE or any other method: UMAP, ICA, NMF etc.

  5. Describe how you might need to group or merge your data to asnwer your question.

  6. End by writing out questions you are still confused about. This doesn’t need to be a full reflection, but come to class ready to ask questions that will help you get your project rolling.

Decision points

  1. use smaller rnaseq datasets ( filtered 6k x 16k) OR use gene P/A
  2. reduce dim of genes OR dim of samples (transpose or not to transpose)
  3. connect to metadata of samples OR of genes
  • red by genes means plotting samples and vv
  • merge rnaseq with sample metadata, use SRX numbers
  • merge gene p/a with annotation, use first_name_comp
  • merge rnaseq with gene annotation use first_name_comp
  1. Choose a color scheme
  2. Does DR technique separate out groups, as seen by color?