Table 3 Table of raw p-values for Welch t-statistics and limma methods using 
and 
from the apoAI control treatment expression data.
and 
from the apoAI control treatment expression data.rank | p-value ( | rank | p-value ( | rank | p-value(limma ( | rank | p-value(limma ( |
|---|---|---|---|---|---|---|---|
1 | 7.3 × 10-7 | 1 | 4.2 × 10-6 | 1 | 3.8 × 10-12 | 1 | 1.5 × 10-9 |
2 | 2.4 × 10-5 | 2 | 2.4 × 10-5 | 4 | 5.2 × 10-7 | 4 | 1.3 × 10-6 |
3 | 3.4 × 10-5 | 4 | 4.0 × 10-5 | 2 | 2.6 × 10-8 | 3 | 1.2 × 10-7 |
4 | 5.0 × 10-5 | 3 | 2.8 × 10-5 | 3 | 5.1 × 10-8 | 2 | 7.6 × 10-8 |
5 | 1.0 × 10-4 | 6 | 1.2 × 10-4 | 5 | 1.4 × 10-6 | 6 | 7.5 × 10 -6 |
6 | 1.0 × 10-4 | 5 | 5.8 × 10-5 | 7 | 9.6 × 10-6 | 7 | 1.2 × 10-5 |
7 | 2.9 × 10-4 | 7 | 2.7 × 10-4 | 12 | 4.5 × 10-5 | 11 | 3.7 × 10-5 |
8 | 5.9 × 10-4 | 9 | 6.4 × 10-4 | 8 | 1.3 × 10-5 | 16 | 4.8 × 10-5 |
9 | 7.4 × 10-4 | 8 | 5.8 × 10-4 | 10 | 1.5 × 10-4 | 61 | 3.3 × 10-4 |
10 | 1.3 × 10-3 | 10 | 1.1 × 10-3 | 6 | 2.0 × 10-6 | 5 | 1.4 × 10-6 |
rank | t-stat ( | rank | t-stat ( | rank | t-stat(limma ( | rank | t-stat(limma ( |
1 | -16.5 | 1 | -12.8 | 1 | -23.1 | 1 | -14.4 |
2 | -9.8 | 2 | -9.8 | 4 | -9.0 | 4 | -8.3 |
3 | -9.3 | 4 | -9.1 | 2 | -11.5 | 3 | -10.1 |
4 | -8.8 | 3 | -9.6 | 3 | -10.9 | 2 | -10.5 |
5 | -7.9 | 6 | -7.7 | 5 | -8.2 | 6 | -7.0 |
6 | -7.8 | 5 | -8.5 | 7 | -6.7 | 7 | -6.7 |
7 | 6.6 | 7 | 6.7 | 12 | 5.9 | 11 | 6.0 |
8 | -5.9 | 9 | -5.8 | 8 | -6.7 | 16 | -5.9 |
9 | -5.7 | 8 | -5.9 | 10 | -5.2 | 61 | -4.8 |
10 | 5.2 | 10 | 5.3 | 6 | 8.0 | 5 | 8.2 |
- The limma method was developed for log-ratios, not proportions, but we show the results using proportions for comparison. The first group of ten rows are the p-values and the second group is the t-statistics, for reference. In the original paper, the top 8 probes were selected using the maxT multiple testing procedure with using Welch t-statistics on
in [12]. This selection is the first column, ranked 1 through 10. The p-values/t-statistics for the probes using 
and limma correspond to the first column, with their ranks shown. Using t-statistics with , the selection is similar to , but not identical, since probes ranked 8th and 9th switch places. Using limma with and , the selection begins to vary widely at the 7th probe.
in [
and limma correspond to the first column, with their ranks shown. Using t-statistics with