Quality Control Progress Summary
- I struggled a little bit with batch correction because I was not sure what arguments to put in the Combat function.
- I had some trouble with my PCA plot because it initially did not indicate any clustering. This issue was resolved by working with my group members and changing the order of the merged data sets.
Summary of work:
- Going through the quality control steps- simpleaffy, QC report, affy quality metrics to identify outliers
- Conducting normalization and batch correction- plotting box plots and PCAs confirm the quality control analysis
- Worked with subgroup to create a presentation and troubleshoot problems in code
- It would be interesting to use other packages to conduct quality control.