Table 1

Summary of statistical test results

Incidences

IQR for ranks
 Known positives achieving rank





TP
 FP
 TN
 FN
 PPV
 Sens
 1st Q
 Median
 3rd Q
Affymetrix Latin Square (known positives per comparison = 14, total, all comparisons = 1274) (rank = 14, maximum achievable positives = 1274)
MAS5
 950
 13,641
 1,134,051
 324
 7%
 75%
 13
 36
 130
 335
dChip PM
 1,068
 14,390
 1,133,302
 206
 7%
 84%
 6
 19
 63
 558
RMA
 1,098
 10,406
 1,137,286
 176
 10%
 86%
 5
 12
 38
 734
logit-Exp
 1,037
 12,311
 1,135,381
 237
 8%
 81%
 6
 15
 53
 636
logit-ExpR
 1,002
 11,667
 1,136,025
 272
 8%
 79%
 6
 15
 69
 619
logit-t
 1,110
 345
 1,147,347
 164
 76%
 87%
 4
 8
 13
 1066






Gene Logic Spike (known positives per comparison = 10, total, all comparisons = 210)
MAS5
 24
 1,305
 263,631
 186
 2%
 11%
 151
 456
 1,283
 10
dChip PM
 38
 1,729
 263,207
 172
 2%
 18%
 72
 255
 1,505
 19
RMA
 91
 1,860
 263,076
 119
 5%
 43%
 21
 112
 450
 41
logit-t
 106
 79
 264,857
 104
 57%
 50%
 4
 8
 21
 151






Gene Logic AML (known positives per comparison = 11, total, all comparisons = 605)
MAS5
 86
 3,473
 690,352
 519
 2%
 14%
 172
 816
 3,952
 21
dChip PM
 84
 3,790
 690,035
 521
 2%
 14%
 64
 703
 5,296
 44
RMA
 199
 3,504
 690,321
 406
 5%
 33%
 15
 330
 5,166
 139
logit-t
 263
 107
 693,718
 342
 71%
 43%
 4
 8
 738
 349






Gene Logic Tonsil (known positives per comparison = 11, total, all comparisons = 726)
MAS5
 239
 5,854
 826,736
 487
 4%
 33%
 35
 127
 681
 81
dChip PM
 307
 3,760
 828,830
 419
 8%
 42%
 12
 49
 418
 180
RMA
 398
 4,693
 827,897
 328
 8%
 55%
 7
 33
 653
 251
logit-t
 490
 1,752
 830,838
 236
 22%
 67%
 3
 7
 15
 524






Gene Logic Tonsil - except two comparisons
MAS5
 234
 4,540
 802,820
 470
 5%
 33%



dChip PM
 295
 2,378
 804,982
 409
 11%
 42%



RMA
 381
 3,263
 804,097
 323
 10%
 54%



logit-t
 473
 116
 807,244
 231
 80%
 67%



Spiked in RNAs are considered positives and all others considered negatives. In the Tonsil dataset, two comparisons resulted in scores much worse than others for all methods (0.75 versus 2 pM and 0.75 versus 75 pM). The last block of results had these comparisons removed. In each block, the first three rows tally t-test results on the MAS5, dChip and RMA indexes with positives having p value < 0.01. Last row tallies t-values of the Logit-t method with positives having |t| > threshold, based on df. Threshold t values correspond approximately to p < 0.01. The first four columns tally calls: TP, true positive; FP, false positive; TN, true negative; FN, false negative. The next two columns indicate performance measures: PPV, positive predictive value TP/(TP+FP); Sens, sensitivity TP/(TP+FN); IQR, Interquartile range for ranks. Ranks of statistics demarking the 1st quartile, median and 3rd quartiles for known positives. The last column shows the number of known positives achieving rank at or below the number of known positives in a comparison. The maximum achievable number for the final column is the total number of known positives for all comparisons.

Lemon et al. Genome Biology 2003 4:R67   doi:10.1186/gb-2003-4-10-r67

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