Table 3.

Table of raw p-values for Welch t-statistics and limma methods using 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.