Bioinformatics- Level 1 Module 3- Irem Agan

Tools: GEO Database, R

Technical Area: Simpleaffy, background correction methods, outliers, R plots,

Soft Skills

  • Reading the more guided document
  • Visualize data


  • Conduct quality control (QC) using Bioconductor packages
  • Produce a QC plot using simpleaffy
  • Researched about background corrections: mas5, RMA, gcrma

Tasks and Obstacles

  • This module was the most challenging for me because there were a lot of terms I was not familiar with. With help of google, I have successfully done it.
  • I choose simpleaffy documentation to produce a QC plot. I spent most of my time researching background correction and normalization.
  • Then I did my batch correction to make my data sets comparable
  • I went with R plots for data visualization and created many visualizations with boxplot, PCA plots, and the correlation heatmap.
  • I was confused with identifying outliers first but then could figure it through some Youtube videos.