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rockefeller cornell mskcc

Introduction to Microarray Analysis and Tools:
[ Course Materials I: Modules A & B (Agnes Viale) ] [ Course Materials II: Module B (Piali Mukherjee) ]

Registration is CLOSED.

Dates: Thursday December 2nd, 2-4pm & Thursday December 9th, 2-4pm (one class in two parts)

Lecture on microarray hybridization technologies, including Affymetrix, spotted arrays and printed oligo arrays, and a survey of some open source and commercial microarray analysis tools.

Organizers: Agnes Viale (GCL, MSKCC), Piali Mukherjee (ICB, WMC)

Size: 50

Module A: Approaches to Microarray-based Studies (day 1: 2 hours)

Part 1: General introduction and potential applications of array platform

  1. Expression profiling
  2. Chromosomal abnormality
  3. Proteomics
  4. Transcription factor binding site analysis
  5. Other applications
Part 2: Overview of existing platforms
  1. Affymetrix platform: technology, principle, pros and cons
  2. Spotted array platform: fabrication process, principle, pros and cons
  3. Other commercially available platforms
Part 3: Experimental design
  1. Types of projects that can benefit from array technology: molecular classification, fishing, others
  2. Technical limitations: starting amount of material, purity of sample
  3. Financial considerations
Part 4: Steps involved in data analysis
  1. Data set QC
  2. Normalization
  3. Feature (gene) filtering
  4. Replicate analysis
  5. Clustering
  6. Statistical tests
  7. Pathways
Part 5: Validation
  1. Real time PCR
  2. Northern blot
  3. RNAse Protection assay

Module B: Survey of Microarray Analysis Tools (day 2: 2 hours)

Part 1: Open-source Tools

  1. Cluster (XCluster) / TreeView
  2. CAGED
  3. D-Chip
  4. Bioconductor (R, S-plus)
  5. Web-based tools (CYBER-T, SNOMAD)

Part 2: Commercial Tools
  1. Genespring
  2. GCOS

Part 3: Introduction to Functional Interpretation of High-throughput Data