2006 GCAT Dry Lab Mini-Workshop
Davidson College
July 17 - 18

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DAY 1
Monday July 17

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• 11 am - overview (Malcolm)
  • Microarray methodology quickly
  • Experimental design
  • Outline the steps required for data analysis
    • probe microarray
    • get slides scanned
    • data are tiff files
    • collect tiff files
    • download gene lists
    • understand spot pattern
    • grid microarray
    • assign gene names to spots
      • genelists
    • determine intensities of spots and generate ratios
    • log-transform data
    • filter irrational data
    • explore data
    • generate multiple time points or conditions (columns)
    • explore/cluster data
      
      
• noon - 1 pm - group lunch. Each person pays for his/her own (remember, we have $0.00 to fund this)
  
  
• 1 pm - 5pm workshop part I (Laurie)
  • Start or resume project
  • Download files from web (download hypothetical data now, for use later)
    • FTP your data here
  • Making sure files are in the right format
  • Loading files into project
  • Linking names to spots (gene lists)
    • 1Grid.xls and 1Grid.txt
    • 4Grid.xls and 4Grid.txt
  • Finding spots (gridding)
    • 1 Grid of Spots (1Red.tif and 1Green.tif)
      24 columns x 23 rows
      
    • 4 Grid of Spots (4Red.tif and 4Green.tif)
      24 columns x 23 rows
      
    
    
  • Distinguish foreground from background (segmentation)
  • Generating ratios (different methods and consequences)
    
• Dinner
  
  
• Homework: we will give you an assignment to work on to have ready for the morning. We will give you access to the computer lab.
  

DAY 2
Tuesday July 18

• checkout of hotels
• 8:30 am - 12:30 workshop part II (Laurie)

  • Start with ratios
  • Merging files (columns/conditions)
    1 Grid data for merging
    4 Grid data for merging
    
  • yeastgenes.info (the yeast gene annotation information file)
  • Exploring data (with limited columns/conditions)
  • Duplicate genes
  • Clustering (recommended method)
    
    
• Spot Synthesizer (for practice and testing; Malcolm)
• Closing comments
• Depart when you are ready

© Copyright 2006 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu