Chapter 6 Exercises

These are intended to be done after completing the worked examples.

6.1 Exercise 1 — https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119732

Using GSE119732,

  1. Map the distribution of the samples as a box plot and a density plot using only the raw data.
  2. Add colours to the plot separating the different variables in the model
  3. Filter out lowly expressed genes and re plot the distributions.

6.2 Exercise 2 — https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122380

Using GSE122380, confirm whether the ID column contains Ensembl IDs with version suffixes.

  1. Map the distribution of the samples as a box plot and a density plot using only the raw data.
  2. Add colours to the plot separating the different variables in the model
  3. Filter out lowly expressed genes and re plot the distributions.

6.3 Exercise 3 -

Can you use the worked example to process the above two GEO records? How?