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

Raw background (BG) (using spots, lowest 4% per block)

   Raw BG (mean)(spots)

2.21

   Raw BG (SD of block means)(spots)

0.16

   Mean of block BG SDs (spots)

0.07

Raw signal

   Raw average signal (all spots)

5.57

   Raw median signal (all spots)

2.10

   Raw average signal/BG ratio

2.52

   Raw median signal/BG ratio

0.95

Scaling factor (SF) (target value = 100), dismissing top 10% and bottom 60%

   SF (using mean)

15.74

Scaled threshold

   Threshold (using mean)

38.63

Percent present (using mean)

   Greater than 1× BG (raw)

54.1

   Greater than threshold (scaled)

50.6

Number of genes different ≥ 1.8 fold (left AND right)

   Total different

43

   Total UP (Cy5/Cy3)

20

   Total DOWN (Cy5/Cy3)

23

Number of genes different ≥ 1.3 fold

   Using mean (1.3)

Number of genes different ≥ 1.8 fold

   Using mean (1.8)

Number of genes different ≥ 3 fold

   Using mean (3)

Number of genes different ≥ 5 fold

   Using mean (5)

Number of genes different ≥ 10 fold

   Using mean (10)

Correlation coefficient

   Cy5 left to Cy5 right (all)

   Cy3 left to Cy3 right (all)

   FC left to FC right (all)

   Average Cy5 to Cy3 (all)