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Table 2 Average AUC for RMA, RMA-noBG, MAS 5.0, dChip, and PLIER for detection of spiked-in genes in the Affymetrix Latin Square spikein experiments, according to the value of d, which is related to the log base 2 fold change between experiments.

From: A distribution-free convolution model for background correction of oligonucleotide microarray data

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
  1. 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.