Data Retrieval and Clustering Summary

• Data Retrieval Options
  
  • Selected Result Sets
    
    • yB8n055 03II01 batch p1 (default result set): weight 1
      
    • yB8n064 03II01 batch p10 (default result set): weight 1
      
    • yB8n065 03II01 batch p11 (default result set): weight 1
      
    • yB8n066 03II01 batch p12 (default result set): weight 1
      
    • yB8n056 03II01 batch p2 (default result set): weight 1
      
    • yB8n057 03II01 batch p3 (default result set): weight 1
      
    • yB8n058 03II01 batch p4 (default result set): weight 1
      
    • yB8n059 03II01 batch p5 (default result set): weight 1
      
    • yB8n060 03II01 batch p6 (default result set): weight 1
      
    • yB8n061 03II01 batch p7 (default result set): weight 1
      
    • yB8n062 03II01 batch p8 (default result set): weight 1
      
    • yB8n063 03II01 batch p9 (default result set): weight 1
      
    • yB8n044 Low-D chemostat vs. High-D chemostat (default result set): weight 1
      
  • Gene Selection: all genes or clones on arrays selected.
    
    • Control spots were not included.
      
    • Empty spots were not included.
      
  • Data Collapse/Retrieval: by SUID.
    
  • Retrieved Log(base2) of R/G Normalized Ratio (Mean)
    
  • Data Filtering Options
    
    • Selected Data Filters:
      
      • Spot is not flagged by experimenter
        
      • Data filters for GENEPIX result sets
        
        • 1: Regression Correlation > 0.6
          
    • 6025 suid(s) passed filters
      
  • Gene Filtering Options (iteration 1)
    
    • Data Distribution Filter: none selected
      
    • Data Transformation/Centering Options
      
      • No centering selected
        
    • Data Value-Based Filter: none selected
      
    • Data Quality (number of spots passing the spot filter criteria)
      
      • Only using genes with > 80% good data
        
        • Filter removed 3915 suid(s), leaving 2110
          
• Clustering Options
  
  • Partitioning: none
    
  • Genes clustered by Pearson Correlation (non-centered metric)
    
  • Arrays clustered by Pearson Correlation (non-centered metric)