Table 2 The effect of choice of gene level statistic and of a corresponding transformation on the detection rate.
From: A general modular framework for gene set enrichment analysis
| Â | no transformation | squared | rank squared | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Â | t | mod.t | corr | t | mod.t | corr | t | mod.t | corr |
set 1 | 0.94 | 0.94 | 0.94 | 0.63 | 0.67 | 0.74 | 0.84 | 0.84 | 0.84 |
set 2 | 1.00 | 1.00 | 1.00 | 0.90 | 0.92 | 0.95 | 1.00 | 1.00 | 1.00 |
set 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 |
set 4 | 0.79 | 0.81 | 0.83 | 0.40 | 0.44 | 0.50 | 0.54 | 0.54 | 0.54 |
set 5 | 0.95 | 0.96 | 0.95 | 0.34 | 0.41 | 0.44 | 0.38 | 0.41 | 0.38 |
set 6 | 0.00 | 0.00 | 0.00 | 0.86 | 0.85 | 0.88 | 0.95 | 0.96 | 0.95 |
set 7 | 0.01 | 0.01 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
set 8 | 0.00 | 0.00 | 0.00 | 0.70 | 0.70 | 0.75 | 0.74 | 0.75 | 0.74 |
set 9 | 0.00 | 0.01 | 0.00 | 0.81 | 0.90 | 0.89 | 0.80 | 0.82 | 0.80 |
| Â | Â | binary | local fdr | Â | Â | ||||
| Â | Â | t | mod.t | corr | t | mod.t | corr | Â | Â |
| Â | set 1 | 0.62 | 0.61 | 0.55 | 0.49 | 0.48 | 0.46 | Â | Â |
| Â | set 2 | 0.81 | 0.87 | 0.73 | 0.77 | 0.78 | 0.71 | Â | Â |
| Â | set 3 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | Â | Â |
| Â | set 4 | 0.38 | 0.44 | 0.34 | 0.32 | 0.36 | 0.32 | Â | Â |
| Â | set 5 | 0.27 | 0.33 | 0.20 | 0.23 | 0.26 | 0.20 | Â | Â |
| Â | set 6 | 0.83 | 0.85 | 0.76 | 0.71 | 0.66 | 0.69 | Â | Â |
| Â | set 7 | 1.00 | 1.00 | 0.99 | 0.99 | 0.99 | 0.95 | Â | Â |
| Â | set 8 | 0.63 | 0.66 | 0.58 | 0.61 | 0.60 | 0.55 | Â | Â |
| Â | set 9 | 0.71 | 0.73 | 0.65 | 0.74 | 0.75 | 0.66 | Â | Â |