StAM Report: Prediction of BCR-ABL (explorative) - beta 0.01, 0.99



Information on Evaluation

Total number of samples: 327
Training samples: 327 ( 15 from BCR-ABL, 312 from other )
Test samples: 327 ( 15 from BCR-ABL, 312 from other )
Focus on class: BCR-ABL
Data frm chip: hgu95av2
Start node: GO:0008150 ( biological_process )


Annotation Information

Chip annotations for: hgu95av2
Chip data package: data package version 1.5.1
Mon May 10 11:12:58 2004
GO data package: GO package version 1.5.1
Mon May 10 11:46:39 2004
Root node chosen: GO:0008150 ( biological_process )
Number of probesets
on the chip:
12625
Probesets annotated
below GO:0008150 :
8679
Number of nodes
with direct annotations:
1359
Total number of nodes: 2204


Information on Cross Validation

Number of samples: 327
Number of classes: 2
Class weights: 'BCR-ABL': 0.01 'other': 0.99
Class prior: 'BCR-ABL':0.046 'other':0.954
Shrinkage candidates: 0, 0.003, 0.006, 0.008, 0.011, 0.014, 0.017, 0.02, 0.023, 0.025, 0.028, 0.031, 0.034, 0.037, 0.039, 0.042, 0.045, 0.048, 0.051, 0.053, 0.056, 0.059, 0.062, 0.065, 0.068, 0.07, 0.073, 0.076, 0.079, 0.082


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
00.015290.091433.13471014423
0.0030.015290.091083.127421014423
0.0060.015290.09073.11761014423
0.0080.015290.090283.11935984371
0.0110.015290.089793.11715984371
0.0140.015290.089243.11557984371
0.0170.015290.088653.10671984371
0.020.015290.088033.12118944363
0.0230.015290.087393.13145924186
0.0250.015290.086823.11909924186
0.0280.015290.086483.15072873900
0.0310.015290.086083.16884853899
0.0340.015290.085763.18113833881
0.0370.015290.085483.19386793751
0.0390.015290.085443.15304783744
0.0420.018350.085473.16072663390
0.0450.018350.086043.25651533351
0.0480.018350.086983.32774453180
0.0510.021410.08693.37348393054
0.0530.021410.085133.4511332295
0.0560.015290.080653.54894251263
0.0590.018350.076773.4428223917
0.0620.027520.074743.747715492
0.0650.018350.072753.9493613439
0.0680.03670.072213.774413439
0.070.018350.071786.873795342
0.0730.015290.071117.290615342
0.0760.024460.101376.513995342
0.0790.085630.1623.883235342


Information on Model Fit


Performance vs. redundancy


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 Best DeltaRoot Error RatePerformanceRedundancy#Nodes#Genes
00.01690.01530.08863.1067984371
0.10.01690.01530.08863.1067984371
0.20.02530.01530.08683.1191924186
0.30.02530.01530.08683.1191924186
0.40.03940.01530.08543.153783744
0.50.05910.01830.07683.442823917
0.60.05910.01830.07683.442823917
0.70.06750.03670.07223.774413439
0.80.06750.03670.07223.774413439
0.90.06750.03670.07223.774413439
10.07320.01530.07117.29065342


Fit for D = 0.0591

Number of classes: 2
Class weights: 'BCR-ABL': 0.01 'other': 0.99
Class prior: 'BCR-ABL':0.046 'other':0.954
Chosen shrinkage level: 0.059
(by accepting the system default (after consulting weighting alternatives) )
Number of nodes left 23
Number of accessible genes 917

Shrunken prediction graph

Hover over a node to see its description, click on it to view its detailed results.


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Nodewise evaluation


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Information on Predictions

Number of samples: 327 (15 from BCR-ABL, 312 from other)
Classes: BCR-ABL, other


Illustration of Performance on testdata

Nodewise evaluation


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Prediction image

Hover over a node description to see its ID, click on it to see detailed results.


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Details on Nodes


GO:0008150

biological_process

Biological
Process

Parent node

8 child nodes

Performance on training data

 SensitivitySpecificity
BCR-ABL0.733330.99679
other0.996790.73333

Performance on test data

 SensitivitySpecificity
BCR-ABL0.733331
other10.73333

Predictions

 ClassBCR-ABLotherPredictionn
BCR-ABL-1 (testset)BCR-ABL0.207450.79255 other
BCR-ABL-2 (testset)BCR-ABL0.701920.29808 BCR-ABL
BCR-ABL-3 (testset)BCR-ABL0.663020.33698 BCR-ABL
BCR-ABL-4 (testset)BCR-ABL0.686170.31383 BCR-ABL
BCR-ABL-5 (testset)BCR-ABL0.568190.43181 BCR-ABL
BCR-ABL-6 (testset)BCR-ABL0.790930.20907 BCR-ABL
BCR-ABL-7 (testset)BCR-ABL0.727810.27219 BCR-ABL
BCR-ABL-8 (testset)BCR-ABL0.6660.334 BCR-ABL
BCR-ABL-9 (testset)BCR-ABL0.207350.79265 other
BCR-ABL-C1 (testset)BCR-ABL0.439440.56056 other
BCR-ABL-Hyperdip-10 (testset)BCR-ABL0.573810.42619 BCR-ABL
BCR-ABL-Hyperdip-R5 (testset)BCR-ABL0.532570.46743 BCR-ABL
BCR-ABL-R1 (testset)BCR-ABL0.327840.67216 other
BCR-ABL-R2 (testset)BCR-ABL0.820290.17971 BCR-ABL
BCR-ABL-R3 (testset)BCR-ABL0.716120.28388 BCR-ABL
E2A-PBX1-10 (testset)other0.005730.99427 other
E2A-PBX1-11 (testset)other0.003060.99694 other
E2A-PBX1-12 (testset)other0.001410.99859 other
E2A-PBX1-13 (testset)other0.002080.99792 other
E2A-PBX1-1 (testset)other0.002260.99774 other
E2A-PBX1-2 (testset)other0.003920.99608 other
E2A-PBX1-3 (testset)other0.00550.9945 other
E2A-PBX1-4 (testset)other0.003710.99629 other
E2A-PBX1-5 (testset)other0.002590.99741 other
E2A-PBX1-6 (testset)other0.001990.99801 other
E2A-PBX1-7 (testset)other0.007480.99252 other
E2A-PBX1-8 (testset)other0.002730.99727 other
E2A-PBX1-9 (testset)other0.001650.99835 other
E2A-PBX1-2M1 (testset)other0.008050.99195 other
E2A-PBX1-C10 (testset)other0.005610.99439 other
E2A-PBX1-C11 (testset)other0.003190.99681 other
E2A-PBX1-C12 (testset)other0.004140.99586 other
E2A-PBX1-C1 (testset)other0.002910.99709 other
E2A-PBX1-C2 (testset)other0.001480.99852 other
E2A-PBX1-C3 (testset)other0.003850.99615 other
E2A-PBX1-C4 (testset)other0.002940.99706 other
E2A-PBX1-C5 (testset)other0.000930.99907 other
E2A-PBX1-C6 (testset)other0.003320.99668 other
E2A-PBX1-C7 (testset)other0.003950.99605 other
E2A-PBX1-C8 (testset)other0.023050.97695 other
E2A-PBX1-C9 (testset)other0.000920.99908 other
E2A-PBX1-R1 (testset)other0.002580.99742 other
Hyperdip-50-10 (testset)other0.066890.93311 other
Hyperdip-50-11 (testset)other0.035640.96436 other
Hyperdip-50-12 (testset)other0.006290.99371 other
Hyperdip-50-13 (testset)other0.015250.98475 other
Hyperdip-50-14 (testset)other0.007710.99229 other
Hyperdip-50-1 (testset)other0.011980.98802 other
Hyperdip-50-2 (testset)other0.010630.98937 other
Hyperdip-50-3 (testset)other0.011270.98873 other
Hyperdip-50-4 (testset)other0.004290.99571 other
Hyperdip-50-5 (testset)other0.020970.97903 other
Hyperdip-50-6 (testset)other0.017440.98256 other
Hyperdip-50-7 (testset)other0.006730.99327 other
Hyperdip-50-8 (testset)other0.012310.98769 other
Hyperdip-50-9 (testset)other0.003830.99617 other
Hyperdip-50-2M1 (testset)other0.198470.80153 other
Hyperdip-50-2M2 (testset)other0.00850.9915 other
Hyperdip-50-C10 (testset)other0.003560.99644 other
Hyperdip-50-C11 (testset)other0.012660.98734 other
Hyperdip-50-C12 (testset)other0.01080.9892 other
Hyperdip-50-C13 (testset)other0.024410.97559 other
Hyperdip-50-C14 (testset)other0.011860.98814 other
Hyperdip-50-C15 (testset)other0.0040.996 other
Hyperdip-50-C16 (testset)other0.005360.99464 other
Hyperdip-50-C17 (testset)other0.008740.99126 other
Hyperdip-50-C18 (testset)other0.0330.967 other
Hyperdip-50-C19 (testset)other0.019930.98007 other
Hyperdip-50-C1 (testset)other0.011970.98803 other
Hyperdip-50-C20 (testset)other0.03810.9619 other
Hyperdip-50-C21 (testset)other0.311960.68804 other
Hyperdip-50-C22 (testset)other0.030540.96946 other
Hyperdip-50-C23 (testset)other0.00730.9927 other
Hyperdip-50-C24 (testset)other0.009590.99041 other
Hyperdip-50-C25 (testset)other0.024420.97558 other
Hyperdip-50-C26 (testset)other0.004970.99503 other
Hyperdip-50-C27-N (testset)other0.006590.99341 other
Hyperdip-50-C28 (testset)other0.004380.99562 other
Hyperdip-50-C29 (testset)other0.015450.98455 other
Hyperdip-50-C2 (testset)other0.005190.99481 other
Hyperdip-50-C30 (testset)other0.02150.9785 other
Hyperdip-50-C31 (testset)other0.07460.9254 other
Hyperdip-50-C32 (testset)other0.488390.51161 other
Hyperdip-50-C33 (testset)other0.001290.99871 other
Hyperdip-50-C34 (testset)other0.053370.94663 other
Hyperdip-50-C35 (testset)other0.030790.96921 other
Hyperdip-50-C36 (testset)other0.223330.77667 other
Hyperdip-50-C37 (testset)other0.014160.98584 other
Hyperdip-50-C38 (testset)other0.085220.91478 other
Hyperdip-50-C39 (testset)other0.008980.99102 other
Hyperdip-50-C3 (testset)other0.005740.99426 other
Hyperdip-50-C40 (testset)other0.006510.99349 other
Hyperdip-50-C41 (testset)other0.006460.99354 other
Hyperdip-50-C42 (testset)other0.011490.98851 other
Hyperdip-50-C43 (testset)other0.001920.99808 other
Hyperdip-50-C4 (testset)other0.030290.96971 other
Hyperdip-50-C5 (testset)other0.007250.99275 other
Hyperdip-50-C6 (testset)other0.041980.95802 other
Hyperdip-50-C7 (testset)other0.395320.60468 other
Hyperdip-50-C8 (testset)other0.009570.99043 other
Hyperdip-50-C9 (testset)other0.00450.9955 other
Hyperdip-50-R1 (testset)other0.04770.9523 other
Hyperdip-50-R2 (testset)other0.007090.99291 other
Hyperdip-50-R3 (testset)other0.002560.99744 other
Hyperdip-50-R4 (testset)other0.014940.98506 other
Hyperdip-50-R5 (testset)other0.147490.85251 other
Hyperdip47-50-1 (testset)other0.357820.64218 other
Hyperdip47-50-2 (testset)other0.042030.95797 other
Hyperdip47-50-3 (testset)other0.004620.99538 other
Hyperdip47-50-2M1 (testset)other0.115230.88477 other
Hyperdip47-50-C10 (testset)other0.012040.98796 other
Hyperdip47-50-C11 (testset)other0.006160.99384 other
Hyperdip47-50-C12 (testset)other0.019360.98064 other
Hyperdip47-50-C13 (testset)other0.004520.99548 other
Hyperdip47-50-C14-N (testset)other0.007230.99277 other
Hyperdip47-50-C15 (testset)other0.007170.99283 other
Hyperdip47-50-C16 (testset)other0.002230.99777 other
Hyperdip47-50-C17 (testset)other0.02030.9797 other
Hyperdip47-50-C18 (testset)other0.012450.98755 other
Hyperdip47-50-C19 (testset)other0.003390.99661 other
Hyperdip47-50-C1 (testset)other0.001850.99815 other
Hyperdip47-50-C2 (testset)other0.120130.87987 other
Hyperdip47-50-C3-N (testset)other0.00930.9907 other
Hyperdip47-50-C4 (testset)other0.004470.99553 other
Hyperdip47-50-C5 (testset)other0.006990.99301 other
Hyperdip47-50-C6 (testset)other0.01450.9855 other
Hyperdip47-50-C7 (testset)other0.002180.99782 other
Hyperdip47-50-C8 (testset)other0.025850.97415 other
Hyperdip47-50-C9 (testset)other0.42670.5733 other
Hypodip-1 (testset)other0.046820.95318 other
Hypodip-2 (testset)other0.006170.99383 other
Hypodip-2M1 (testset)other0.036750.96325 other
Hypodip-C1 (testset)other0.027060.97294 other
Hypodip-C2 (testset)other0.004560.99544 other
Hypodip-C3 (testset)other0.020510.97949 other
Hypodip-C4 (testset)other0.007990.99201 other
Hypodip-C5 (testset)other0.042930.95707 other
Hypodip-C6 (testset)other0.019910.98009 other
MLL-1 (testset)other0.003070.99693 other
MLL-2 (testset)other0.001860.99814 other
MLL-3 (testset)other0.039810.96019 other
MLL-4 (testset)other0.002780.99722 other
MLL-5 (testset)other0.015430.98457 other
MLL-6 (testset)other0.00770.9923 other
MLL-7 (testset)other0.006750.99325 other
MLL-8 (testset)other0.005090.99491 other
MLL-2M1 (testset)other0.005320.99468 other
MLL-2M2 (testset)other0.005940.99406 other
MLL-C1 (testset)other0.003920.99608 other
MLL-C2 (testset)other0.020560.97944 other
MLL-C3 (testset)other0.005290.99471 other
MLL-C4 (testset)other0.003570.99643 other
MLL-C5 (testset)other0.003980.99602 other
MLL-C6 (testset)other0.002140.99786 other
MLL-R1 (testset)other0.004230.99577 other
MLL-R2 (testset)other0.003460.99654 other
MLL-R3 (testset)other0.004430.99557 other
MLL-R4 (testset)other0.005820.99418 other
Normal-1 (testset)other0.001960.99804 other
Normal-2 (testset)other0.187350.81265 other
Normal-3 (testset)other0.122160.87784 other
Normal-C1-N (testset)other0.006020.99398 other
Normal-C10 (testset)other0.007280.99272 other
Normal-C11-N (testset)other0.004390.99561 other
Normal-C12 (testset)other0.001690.99831 other
Normal-C2-N (testset)other0.00510.9949 other
Normal-C3-N (testset)other0.00270.9973 other
Normal-C4-N (testset)other0.002750.99725 other
Normal-C5 (testset)other0.012520.98748 other
Normal-C6 (testset)other0.009120.99088 other
Normal-C7-N (testset)other0.003690.99631 other
Normal-C8 (testset)other0.073690.92631 other
Normal-C9 (testset)other0.02590.9741 other
Normal-R1 (testset)other0.176160.82384 other
Normal-R2-N (testset)other0.01290.9871 other
Normal-R3 (testset)other0.003950.99605 other
Pseudodip-1 (testset)other0.108660.89134 other
Pseudodip-2 (testset)other0.011770.98823 other
Pseudodip-3 (testset)other0.029010.97099 other
Pseudodip-4 (testset)other0.038950.96105 other
Pseudodip-5 (testset)other0.02160.9784 other
Pseudodip-6 (testset)other0.026390.97361 other
Pseudodip-7 (testset)other0.230950.76905 other
Pseudodip-8-N (testset)other0.004440.99556 other
Pseudodip-9 (testset)other0.049050.95095 other
Pseudodip-C10 (testset)other0.015350.98465 other
Pseudodip-C11 (testset)other0.087340.91266 other
Pseudodip-C12 (testset)other0.019660.98034 other
Pseudodip-C13 (testset)other0.013290.98671 other
Pseudodip-C14 (testset)other0.165270.83473 other
Pseudodip-C15 (testset)other0.007490.99251 other
Pseudodip-C16-N (testset)other0.014270.98573 other
Pseudodip-C17 (testset)other0.011540.98846 other
Pseudodip-C18 (testset)other0.013280.98672 other
Pseudodip-C19 (testset)other0.046770.95323 other
Pseudodip-C1 (testset)other0.025230.97477 other
Pseudodip-C2-N (testset)other0.002680.99732 other
Pseudodip-C3 (testset)other0.002890.99711 other
Pseudodip-C4 (testset)other0.003340.99666 other
Pseudodip-C5 (testset)other0.012990.98701 other
Pseudodip-C6 (testset)other0.031710.96829 other
Pseudodip-C7 (testset)other0.02210.9779 other
Pseudodip-C8 (testset)other0.005670.99433 other
Pseudodip-C9 (testset)other0.036140.96386 other
Pseudodip-R1-N (testset)other0.008080.99192 other
T-ALL-10 (testset)other0.001660.99834 other
T-ALL-1 (testset)other0.008110.99189 other
T-ALL-2 (testset)other0.001830.99817 other
T-ALL-3 (testset)other0.074330.92567 other
T-ALL-4 (testset)other0.005880.99412 other
T-ALL-5 (testset)other0.000830.99917 other
T-ALL-6 (testset)other0.004340.99566 other
T-ALL-7 (testset)other0.004790.99521 other
T-ALL-8 (testset)other0.006910.99309 other
T-ALL-9 (testset)other0.031080.96892 other
T-ALL-2M1 (testset)other0.057960.94204 other
T-ALL-C10 (testset)other0.004450.99555 other
T-ALL-C11 (testset)other0.084350.91565 other
T-ALL-C12 (testset)other0.004450.99555 other
T-ALL-C13 (testset)other0.012360.98764 other
T-ALL-C14 (testset)other0.005340.99466 other
T-ALL-C15 (testset)other0.02590.9741 other
T-ALL-C16 (testset)other0.001790.99821 other
T-ALL-C17 (testset)other0.012310.98769 other
T-ALL-C18 (testset)other0.003420.99658 other
T-ALL-C19 (testset)other0.047160.95284 other
T-ALL-C1 (testset)other0.01980.9802 other
T-ALL-C20 (testset)other0.010290.98971 other
T-ALL-C21 (testset)other0.028490.97151 other
T-ALL-C22 (testset)other0.007940.99206 other
T-ALL-C23 (testset)other0.006940.99306 other
T-ALL-C24 (testset)other0.001670.99833 other
T-ALL-C25 (testset)other0.003870.99613 other
T-ALL-C26 (testset)other0.003240.99676 other
T-ALL-C2 (testset)other0.023710.97629 other
T-ALL-C3 (testset)other0.005130.99487 other
T-ALL-C4 (testset)other0.010780.98922 other
T-ALL-C5 (testset)other0.007240.99276 other
T-ALL-C6 (testset)other0.004550.99545 other
T-ALL-C7 (testset)other0.002990.99701 other
T-ALL-C8 (testset)other0.003690.99631 other
T-ALL-C9 (testset)other0.00740.9926 other
T-ALL-R1 (testset)other0.002230.99777 other
T-ALL-R2 (testset)other0.066420.93358 other
T-ALL-R3 (testset)other0.004640.99536 other
T-ALL-R4 (testset)other0.006130.99387 other
T-ALL-R5 (testset)other0.044160.95584 other
T-ALL-R6 (testset)other0.013410.98659 other
TEL-AML1-10 (testset)other0.021710.97829 other
TEL-AML1-11 (testset)other0.006860.99314 other
TEL-AML1-12 (testset)other0.00640.9936 other
TEL-AML1-13 (testset)other0.008660.99134 other
TEL-AML1-14 (testset)other0.006260.99374 other
TEL-AML1-1 (testset)other0.003550.99645 other
TEL-AML1-2 (testset)other0.010740.98926 other
TEL-AML1-3 (testset)other0.016370.98363 other
TEL-AML1-4 (testset)other0.010020.98998 other
TEL-AML1-5 (testset)other0.001930.99807 other
TEL-AML1-6 (testset)other0.003930.99607 other
TEL-AML1-7 (testset)other0.008150.99185 other
TEL-AML1-8 (testset)other0.003080.99692 other
TEL-AML1-9 (testset)other0.016490.98351 other
TEL-AML1-2M1 (testset)other0.181690.81831 other
TEL-AML1-2M2 (testset)other0.009980.99002 other
TEL-AML1-2M3 (testset)other0.008150.99185 other
TEL-AML1-2M4 (testset)other0.006930.99307 other
TEL-AML1-2M5 (testset)other0.006970.99303 other
TEL-AML1-C10 (testset)other0.00670.9933 other
TEL-AML1-C11 (testset)other0.043750.95625 other
TEL-AML1-C12 (testset)other0.00280.9972 other
TEL-AML1-C13 (testset)other0.006270.99373 other
TEL-AML1-C14 (testset)other0.01180.9882 other
TEL-AML1-C15 (testset)other0.008040.99196 other
TEL-AML1-C16 (testset)other0.03860.9614 other
TEL-AML1-C17 (testset)other0.00410.9959 other
TEL-AML1-C18 (testset)other0.026210.97379 other
TEL-AML1-C19 (testset)other0.005350.99465 other
TEL-AML1-C1 (testset)other0.006890.99311 other
TEL-AML1-C20 (testset)other0.012610.98739 other
TEL-AML1-C21 (testset)other0.013220.98678 other
TEL-AML1-C22 (testset)other0.012980.98702 other
TEL-AML1-C23 (testset)other0.004320.99568 other
TEL-AML1-C24 (testset)other0.012020.98798 other
TEL-AML1-C25 (testset)other0.006740.99326 other
TEL-AML1-C26 (testset)other0.014180.98582 other
TEL-AML1-C27 (testset)other0.009180.99082 other
TEL-AML1-C28 (testset)other0.006750.99325 other
TEL-AML1-C29 (testset)other0.00840.9916 other
TEL-AML1-C2 (testset)other0.011090.98891 other
TEL-AML1-C30 (testset)other0.011880.98812 other
TEL-AML1-C31 (testset)other0.0150.985 other
TEL-AML1-C32 (testset)other0.017740.98226 other
TEL-AML1-C33 (testset)other0.002130.99787 other
TEL-AML1-C34 (testset)other0.010590.98941 other
TEL-AML1-C35 (testset)other0.024550.97545 other
TEL-AML1-C36 (testset)other0.004740.99526 other
TEL-AML1-C37 (testset)other0.01220.9878 other
TEL-AML1-C38 (testset)other0.029750.97025 other
TEL-AML1-C39 (testset)other0.003980.99602 other
TEL-AML1-C3 (testset)other0.011010.98899 other
TEL-AML1-C40 (testset)other0.007350.99265 other
TEL-AML1-C41 (testset)other0.005190.99481 other
TEL-AML1-C42 (testset)other0.006350.99365 other
TEL-AML1-C43 (testset)other0.004970.99503 other
TEL-AML1-C44 (testset)other0.0080.992 other
TEL-AML1-C45 (testset)other0.005920.99408 other
TEL-AML1-C46 (testset)other0.014590.98541 other
TEL-AML1-C47 (testset)other0.007080.99292 other
TEL-AML1-C48 (testset)other0.031660.96834 other
TEL-AML1-C49 (testset)other0.010190.98981 other
TEL-AML1-C4 (testset)other0.004270.99573 other
TEL-AML1-C50 (testset)other0.006780.99322 other
TEL-AML1-C51 (testset)other0.029250.97075 other
TEL-AML1-C52 (testset)other0.038030.96197 other
TEL-AML1-C53 (testset)other0.034680.96532 other
TEL-AML1-C54 (testset)other0.007030.99297 other
TEL-AML1-C55 (testset)other0.003680.99632 other
TEL-AML1-C56 (testset)other0.003590.99641 other
TEL-AML1-C57 (testset)other0.003910.99609 other
TEL-AML1-C5 (testset)other0.016760.98324 other
TEL-AML1-C6 (testset)other0.003940.99606 other
TEL-AML1-C7 (testset)other0.007320.99268 other
TEL-AML1-C8 (testset)other0.002240.99776 other
TEL-AML1-C9 (testset)other0.007350.99265 other
TEL-AML1-R1 (testset)other0.001770.99823 other
TEL-AML1-R2 (testset)other0.066060.93394 other
TEL-AML1-R3 (testset)other0.010990.98901 other

 


Generated by StAM on Tue Sep 7 18:31:49 2004