Table 1 |
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Summary view of cDNA array data from the custom cDNA normalization program |
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|
Values |
Cy5 |
Cy3 |
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|
|
|
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|
Left |
Right |
Left |
Right |
|
|
|
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Raw background (BG) (using spots, lowest 4% per block) |
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|
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 |
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|
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% |
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|
SF (using mean) |
25.18 |
25.87 |
17.37 |
15.74 |
|
Scaled threshold |
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|
Threshold (using mean) |
41.55 |
38.63 |
41.55 |
38.63 |
|
Percent present (using mean) |
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|
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) |
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|
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 |
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|
Using mean (1.3) |
303 |
Percent |
7.3 |
|
|
Number of genes different ≥ 1.8 fold |
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|
Using mean (1.8) |
204 |
Percent |
4.5 |
|
|
Number of genes different ≥ 3 fold |
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|
Using mean (3) |
68 |
Percent |
1.3 |
|
|
Number of genes different ≥ 5 fold |
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|
Using mean (5) |
28 |
Percent |
0.6 |
|
|
Number of genes different ≥ 10 fold |
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|
Using mean (10) |
5 |
Percent |
0.1 |
|
|
Correlation coefficient |
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|
Cy5 left to Cy5 right (all) |
0.989 |
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|
Cy3 left to Cy3 right (all) |
0.984 |
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|
FC left to FC right (all) |
0.968 |
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|
Average Cy5 to Cy3 (all) |
0.705 |
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|
|
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|
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. |
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|
Zapala et al. Genome Biology 2002 3:software0001.1 doi:10.1186/gb-2002-3-6-software0001 |
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