The workshop will cover installation of a new genome; import, pre-process data, visualization, and filtering of microarray data; and basic statistical analysis, hierarchical clustering, class prediction and pathway analysis.

Course Materials

1. Importing data (Julia Zhao; 92 KB PDF)
2. Data processing (Jenny Xiang; 331 KB PDF)
3. Visualization (Agnes Viale; 1.2 MB PDF)
4. Filtering data (Agnes Viale; 406 KB PDF)
5. Statistical analysis (Jenny Xiang; 126 KB PDF)
6. Clustering (Julia Zhao; 171 KB PDF)
7. Pathway analysis (Jenny Xiang; 327 KB PDF)

Hands-on computer based workshop on a popular microarray data analysis software package covering installation of a new genomes, import visualization and filtering of data, basic statistical analysis, hierarchical clustering, class prediction and pathway analysis. Preference will be given to individuals with microarray data to analyze.

Organizers: Agnes Viale (GCL, MSKCC), Jenny Xiang (Microarray Core, WMC)

Size: 10

Schedule:

1. Installation of genomes
   1. Affymetrix
   2. Others
2. Data import
   1. Experiments parameters
   2. Normalization
   3. Interpretation
3. Data visualization
   1. Ordered list
   2. Graph view
   3. Spreadsheet view
   4. Scatter plot
   5. Tree view
4. Gene filtering
   1. On expression values
   2. On fold change
   3. On flags
5. Basic statistical analysis
   1. One-way Anova (T-test)
   2. Two-way Anova
6. Hierarchical clustering
   1. Condition tree
   2. Gene tree
7. Class prediction: overview
8. Pathway analysis: overview

Prerequisite: Microarray data to analyze.