Self-Assessment: Module 4 Maryam Momeni

Module 4

Technical area:

  • Collaborating in testing the Shiny app
  • Removing outliers from datasets
  • Getting the annotations from Databases
  • Removing duplicated Probe IDs and the genes which don’t have any corresponding Probe IDs
  • Selecting a representative row from the rows with duplicated Symbols
  • Filtering out genes below the 2nd percentile of the expression distribution of the dataset
  • Differential expression analysis by Limma package
  • Plotting a volcano plot in which the differentially expressed genes are identified
  • Plotting a Heatmap with expression values of the top 50 most significant genes

Soft skills:

  • Presenting a presentation on teaching the codes in detail to the others
  • Troubleshooting the Errors that I was being got from implementing the codes


  • hgu133plus2.db
  • limma package
  • EnhancedVolcano package


  • Obtaining the list of differentially expressed genes of Colorectal cancer
  • Plotting Volcano plot and heatmap on the expression values of differentially expressed genes
  • Preparing a presentation on module 4


I had some problems in removing duplicated Prob IDs, removing genes that were not mapped to any symbols, and selecting a representative for rows with duplicated Symbols. That was fixed by searching for different tutorials and different sites on the net.