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Table 1 Summary view of cDNA array data from the custom cDNA normalization program

From: Software and methods for oligonucleotide and cDNA array data analysis

Values Cy5 Cy3
  Left Right Left Right
Raw background (BG) (using spots, lowest 4% per block)     
   Raw BG (mean)(spots) 0.64 0.65 2.20 2.21
   Raw BG (SD of block means)(spots) 0.04 0.03 0.22 0.16
   Mean of block BG SDs (spots) 0.03 0.02 0.08 0.07
Raw signal     
   Raw average signal (all spots) 3.73 3.65 5.01 5.57
   Raw median signal (all spots) 1.24 1.18 1.94 2.10
   Raw average signal/BG ratio 5.79 5.58 2.28 2.52
   Raw median signal/BG ratio 1.92 1.81 0.88 0.95
Scaling factor (SF) (target value = 100), dismissing top 10% and bottom 60%     
   SF (using mean) 25.18 25.87 17.37 15.74
Scaled threshold     
   Threshold (using mean) 41.55 38.63 41.55 38.63
Percent present (using mean)     
   Greater than 1× BG (raw) 72.0 70.6 51.4 54.1
   Greater than threshold (scaled) 47.5 48.5 48.9 50.6
Number of genes different ≥ 1.8 fold (left AND right)     
   Total different Using mean 43 Using median 43
   Total UP (Cy5/Cy3) Using mean 20 Using median 20
   Total DOWN (Cy5/Cy3) Using mean 23 Using median 23
Number of genes different ≥ 1.3 fold     
   Using mean (1.3) 303 Percent 7.3  
Number of genes different ≥ 1.8 fold     
   Using mean (1.8) 204 Percent 4.5  
Number of genes different ≥ 3 fold     
   Using mean (3) 68 Percent 1.3  
Number of genes different ≥ 5 fold     
   Using mean (5) 28 Percent 0.6  
Number of genes different ≥ 10 fold     
   Using mean (10) 5 Percent 0.1  
Correlation coefficient     
   Cy5 left to Cy5 right (all) 0.989    
   Cy3 left to Cy3 right (all) 0.984    
   FC left to FC right (all) 0.968    
   Average Cy5 to Cy3 (all) 0.705    
  1. The cDNA data summary file provides an assessment of the data quality and a summary of the overall results for each cDNA array experiment. Crucial information is provided in a simple table format that prints to a single page. Below the single page summary, but not shown in the figure, are the detailed results for each spot on the cDNA array. The results for each spot (or gene) include an absolute call of present (P) or absent (A), the background subtracted and scaled intensity, the difference between the scaled fluorophore intensities, the fold change, and a qualitative difference or change call of I, MI, D or MD, which is based on the fold changes across the duplicate spot data. The spot-by-spot results file is read and analyzed by the Spot software program.