Table 2.
d | DFCM | RMA | RMA-noBG | MAS 5 | dChip | PLIER |
Average AUC for the HG-U95Av2 Latin Square Spike-In Data Set | ||||||
1 | 0.732 | 0.715 | 0.721 | 0.063 | 0.572 | 0.062 |
2 | 0.871 | 0.869 | 0.918 | 0.167 | 0.803 | 0.316 |
3 | 0.936 | 0.935 | 0.935 | 0.484 | 0.886 | 0.629 |
4 | 0.997 | 0.994 | 0.986 | 0.798 | 0.948 | 0.769 |
5 | 1.000 | 0.999 | 0.999 | 0.916 | 0.980 | 0.853 |
6 | 1.000 | 1.000 | 1.000 | 0.967 | 0.987 | 0.876 |
7 | 1.000 | 1.000 | 1.000 | 0.981 | 0.999 | 0.876 |
Average AUC for the HG-U133A Latin Square Spike-In Data Set | ||||||
1 | 0.768 | 0.738 | 0.734 | 0.060 | 0.600 | 0.365 |
2 | 0.858 | 0.831 | 0.812 | 0.307 | 0.709 | 0.752 |
3 | 0.935 | 0.904 | 0.908 | 0.561 | 0.811 | 0.883 |
4 | 0.934 | 0.964 | 0.964 | 0.837 | 0.913 | 0.951 |
5 | 0.983 | 0.990 | 0.983 | 0.939 | 0.971 | 0.985 |
6 | 0.999 | 0.998 | 0.996 | 0.968 | 0.989 | 0.994 |
7 | 0.999 | 0.999 | 0.999 | 0.978 | 0.972 | 0.996 |
Larger values of d correspond to larger fold changes among spiked-in transcripts between pairs of experiments. Eighteen spike-in probes sets were used for the HG-U95Av2 experiment, and 64 spiked-in probe sets were used for the HG-U133A to calculate true and false positives, as discussed in Methods. To calculate the AUCs, the number of false positives was set to 100 for the HG-U95Av2 experiment, and 200 for the HG-U133a experiment. Numbers in bold indicate the best value for each row.