Tools: GEO Database, R
Technical Area: Simpleaffy, background correction methods, outliers, R plots,
- 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.