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Table 1 Area under ROC curves up to 100 false positives, RMA and GCRMA

From: Empirical Bayes models for multiple probe type microarrays at the probe level

Method Pre-processing Affymetrix U95 Affymetrix 133A Golden Spike Gene Logic Tonsil Gene Logic AML
PLW RMA 96(1) 93(6) 42(1) 87(1) 86(1)
LMW RMA 96(2) 94(1) 36(5) 84(3) 80(5)
LPE RMA 94(7) 93(11) 40(2) 84(2) 85(2)
combined-p RMA 95(4) 92(12) 39(3) 83(4) 81(4)
WAME RMA 95(5) 94(2) 33(7) 81(7) 78(8)
median-t RMA 95(3) 93(10) 39(4) 82(6) 80(6)
IBMT RMA 95(6) 94(3) 34(6) 78(9) 76(9)
Efron-t RMA 94(8) 93(4) 32(8) 79(8) 79(7)
FC RMA 92(12) 93(5) 29(12) 83(5) 85(3)
LIMMA RMA 94(9) 93(7) 32(9) 76(10) 75(10)
SAM RMA 94(10) 93(8) 32(11) 74(12) 74(11)
Shrink-t RMA 94(11) 93(9) 32(10) 75(11) 73(12)
t-test RMA 85(13) 86(13) 21(13) 57(13) 52(13)
PLW GCRMA 97(1) 92(8) 54(1) 87(1) 87(1)
LMW GCRMA 95(3) 93(1) 50(5) 84(3) 79(6)
median-t GCRMA 96(2) 92(10) 50(2) 83(4) 81(5)
combined-p GCRMA 95(5) 91(12) 50(4) 86(2) 81(4)
LPE GCRMA 95(6) 91(11) 50(3) 82(6) 86(2)
IBMT GCRMA 95(4) 93(2) 47(6) 81(9) 76(8)
Efron-t GCRMA 94(7) 93(4) 37(8) 82(7) 79(7)
WAME GCRMA 94(10) 93(3) 39(7) 83(5) 75(10)
FC GCRMA 93(12) 93(7) 30(13) 81(8) 86(3)
LIMMA GCRMA 94(9) 93(5) 37(9) 80(10) 73(11)
SAM GCRMA 94(8) 93(6) 36(11) 79(11) 76(9)
Shrink-t GCRMA 94(11) 92(9) 37(10) 78(12) 70(12)
t-test GCRMA 86(13) 84(13) 30(12) 64(13) 53(13)
  1. Area under ROC curves up to 100 false positives rounded to nearest integer value with an optimum of 100. Numbers within parenthesis are within data set ranks for the methods compared (separately for RMA and GCRMA). Methods are ordered with respect to mean rank across the five data sets. Results in the upper and lower part are based on RMA and GCRMA pre-processed data, respectively.