This report correspond to the project for the class Stat597A Bioinformatics for High Throuhput Experiments during the Spring semester in 2014. The project is a collaboration between Yong Jung (YJ) & Hannier Pulido (HP).

The following is the workflow of the data analysis and the person responsible for each step:

1. Access to CEL files (YJ & HP)

2. Quality Assessment on raw data (HP)

   • RNA degradation plots
   • Boxplots
   • Density plots

3. Preprocess data (YJ & HP)

   • Background correction and normalization
   • Filtering absent genes
   • Remove outliers and unidentified groups

4. Preliminary analysis (YJ)

   • K-means clustering

5. Quality assessment of filtered data (HP)

   • Boxplots
   • Density plots
   • MVA plots

6. Exploratory analysis (YJ & HP)

   • K-means clustering
   • HCA
   • PCA

7. Random Forest for feature selection (HP)

8. Visualization of results (YJ & HP)

9. Functional enrichment analysis using Gene Ontology (YJ)

10. Literature review using the GO terms (YJ & HP)