Table 3.
Assessment results
| Accuracy |
Precision |
Performance |
||||
|---|---|---|---|---|---|---|
| Platform | Slope (SD) | SD | 99.5% | SNR | POT | GNN |
| Low | ||||||
| Affymetrix (RMA) | 0.20 (0.31) | 0.10 | 0.36 | 2.00 | 0.30 | 13 |
| Affymetrix (MAS5) | 0.58 (0.73) | 0.64 | 3.54 | 0.91 | 0.00 | 581 |
| Agilent | 0.26 (0.90) | 0.40 | 2.74 | 0.65 | 0.00 | 246 |
| Illumina | 0.11 (0.39) | 0.35 | 1.18 | 0.31 | 0.00 | 506 |
| Medium | ||||||
| Affymetrix (RMA) | 0.79 (0.35) | 0.09 | 0.40 | 8.78 | 0.87 | 19 |
| Affymetrix (MAS5) | 0.80 (0.38) | 0.18 | 0.95 | 4.44 | 0.35 | 24 |
| Agilent | 0.99 (0.17) | 0.11 | 0.86 | 9.00 | 0.78 | 20 |
| Illumina | 1.15 (0.37) | 0.25 | 1.48 | 4.60 | 0.19 | 25 |
| High | ||||||
| Affymetrix (RMA) | 0.57 (0.15) | 0.06 | 0.22 | 9.50 | 0.99 | 10 |
| Affymetrix (MAS5) | 0.48 (0.19) | 0.13 | 0.42 | 3.69 | 0.62 | 10 |
| Agilent | 0.61 (0.29) | 0.10 | 0.38 | 6.10 | 0.79 | 10 |
| Illumina | 0.42 (0.32) | 0.15 | 0.62 | 2.80 | 0.27 | 15 |
For each of the ALE strata, we report summary assessments for accuracy, precision and overall performance. The first column shows the signal detection slope, which can be interpreted as the expected observed difference when the true difference is a fold change of 2. In parenthesis is the SD of the log-ratios associated with nonzero nominal log-ratios. The second column shows the standard deviation of null log-ratios. The SD can be interpreted as the expected range of observed log-ratios for genes that are not differentially expressed. The third column shows the 99.5th percentile of the null distribution. It can be interpreted as the expected minimum value that the top 100 nondifferentially expressed genes will reach. The fourth column shows the ratio of the values in column 1 and column 2. It is a rough measure of signal to noise ratio. The fifth column shows the probability that, when comparing two samples, a gene with a true log-fold change of 2 will appear in a list of the 100 genes with the highest log-ratios. The sixth column shows the size of gene list necessary to obtain 10 true positives when one considers a list of genes with the highest fold change.