StAM Report: Prediction of BCR-ABL (predictive) - beta 0.046, 0.954



Information on Evaluation

Total number of samples: 327
Training samples: 218 ( 10 from BCR-ABL, 208 from other )
Test samples: 109 ( 5 from BCR-ABL, 104 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: 218
Number of classes: 2
Class weights: 'BCR-ABL': 0.046 'other': 0.954
Class prior: 'BCR-ABL':0.046 'other':0.954
Shrinkage candidates: 0, 0.009, 0.017, 0.026, 0.034, 0.043, 0.052, 0.06, 0.069, 0.078, 0.086, 0.095, 0.103, 0.112, 0.121, 0.129, 0.138, 0.147, 0.155, 0.164, 0.172, 0.181, 0.19, 0.198, 0.207, 0.216, 0.224, 0.233, 0.241, 0.25


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
00.03670.152483.49579893979
0.0090.03670.152423.49655893979
0.0170.03670.152353.49743893979
0.0260.03670.152273.49595893979
0.0340.03670.152183.49412893979
0.0430.03670.152053.49081893979
0.0520.03670.151883.49182893979
0.060.027520.151713.50032873928
0.0690.027520.151523.50145873928
0.0780.027520.151333.53159853927
0.0860.027520.151163.53339853927
0.0950.027520.150973.53522853927
0.1030.027520.150733.53754853927
0.1120.027520.150473.54048853927
0.1210.027520.150183.54442853927
0.1290.027520.149863.53742853927
0.1380.027520.149573.54085833690
0.1470.027520.14923.51917793685
0.1550.027520.148563.48745773617
0.1640.022940.147613.65328563267
0.1720.022940.145813.66041503254
0.1810.009170.143273.70084402039
0.190.009170.139713.82569342006
0.1980.009170.140413.83257342006
0.2070.009170.141893.71968321907
0.2160.018350.141924.2940420515
0.2240.018350.134354.0148320515
0.2330.027520.126334.6724811102
0.2410.022940.157694.4911911102


Information on Model Fit


Fit for D = 0.181

Number of classes: 2
Class weights: 'BCR-ABL': 0.046 'other': 0.954
Class prior: 'BCR-ABL':0.046 'other':0.954
Chosen shrinkage level: 0.181
(by optimizing the root's error rate )
Number of nodes left 40
Number of accessible genes 2039

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)
Test samples: 109 (5 from BCR-ABL, 104 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-ABL0.51
other10.5

Performance on test data

 SensitivitySpecificity
BCR-ABL01
other10

Predictions

 ClassBCR-ABLotherPredictionn
BCR-ABL-1BCR-ABL0.280940.71906 other
BCR-ABL-2 (testset)BCR-ABL0.335420.66458 other
BCR-ABL-3 (testset)BCR-ABL0.396320.60368 other
BCR-ABL-4BCR-ABL0.661570.33843 BCR-ABL
BCR-ABL-5 (testset)BCR-ABL0.100880.89912 other
BCR-ABL-6BCR-ABL0.80810.1919 BCR-ABL
BCR-ABL-7BCR-ABL0.581080.41892 BCR-ABL
BCR-ABL-8BCR-ABL0.689540.31046 BCR-ABL
BCR-ABL-9BCR-ABL0.173520.82648 other
BCR-ABL-C1 (testset)BCR-ABL0.15960.8404 other
BCR-ABL-Hyperdip-10BCR-ABL0.376710.62329 other
BCR-ABL-Hyperdip-R5BCR-ABL0.282160.71784 other
BCR-ABL-R1BCR-ABL0.46460.5354 other
BCR-ABL-R2BCR-ABL0.806120.19388 BCR-ABL
BCR-ABL-R3 (testset)BCR-ABL0.278520.72148 other
E2A-PBX1-10other0.004750.99525 other
E2A-PBX1-11other0.00190.9981 other
E2A-PBX1-12other0.001340.99866 other
E2A-PBX1-13other0.004430.99557 other
E2A-PBX1-1 (testset)other0.003160.99684 other
E2A-PBX1-2other0.004850.99515 other
E2A-PBX1-3other0.00380.9962 other
E2A-PBX1-4other0.006180.99382 other
E2A-PBX1-5other0.003840.99616 other
E2A-PBX1-6other0.003090.99691 other
E2A-PBX1-7other0.003670.99633 other
E2A-PBX1-8other0.003340.99666 other
E2A-PBX1-9other0.001850.99815 other
E2A-PBX1-2M1other0.002370.99763 other
E2A-PBX1-C10 (testset)other0.009960.99004 other
E2A-PBX1-C11 (testset)other0.001330.99867 other
E2A-PBX1-C12other0.006680.99332 other
E2A-PBX1-C1other0.003630.99637 other
E2A-PBX1-C2other0.001860.99814 other
E2A-PBX1-C3other0.004450.99555 other
E2A-PBX1-C4other0.002350.99765 other
E2A-PBX1-C5 (testset)other0.001120.99888 other
E2A-PBX1-C6other0.00240.9976 other
E2A-PBX1-C7other0.003910.99609 other
E2A-PBX1-C8other0.017850.98215 other
E2A-PBX1-C9other0.000820.99918 other
E2A-PBX1-R1other0.001930.99807 other
Hyperdip-50-10other0.029580.97042 other
Hyperdip-50-11other0.036990.96301 other
Hyperdip-50-12 (testset)other0.009840.99016 other
Hyperdip-50-13other0.026510.97349 other
Hyperdip-50-14 (testset)other0.044590.95541 other
Hyperdip-50-1other0.021930.97807 other
Hyperdip-50-2other0.035660.96434 other
Hyperdip-50-3 (testset)other0.027190.97281 other
Hyperdip-50-4 (testset)other0.030070.96993 other
Hyperdip-50-5other0.024590.97541 other
Hyperdip-50-6other0.039530.96047 other
Hyperdip-50-7other0.012060.98794 other
Hyperdip-50-8other0.042390.95761 other
Hyperdip-50-9other0.010930.98907 other
Hyperdip-50-2M1other0.022180.97782 other
Hyperdip-50-2M2 (testset)other0.005020.99498 other
Hyperdip-50-C10 (testset)other0.004570.99543 other
Hyperdip-50-C11other0.028920.97108 other
Hyperdip-50-C12other0.015870.98413 other
Hyperdip-50-C13 (testset)other0.119470.88053 other
Hyperdip-50-C14 (testset)other0.01760.9824 other
Hyperdip-50-C15 (testset)other0.007820.99218 other
Hyperdip-50-C16other0.009240.99076 other
Hyperdip-50-C17other0.036970.96303 other
Hyperdip-50-C18 (testset)other0.071710.92829 other
Hyperdip-50-C19other0.071920.92808 other
Hyperdip-50-C1 (testset)other0.021830.97817 other
Hyperdip-50-C20other0.067490.93251 other
Hyperdip-50-C21other0.112750.88725 other
Hyperdip-50-C22other0.034150.96585 other
Hyperdip-50-C23other0.010860.98914 other
Hyperdip-50-C24 (testset)other0.022520.97748 other
Hyperdip-50-C25other0.076490.92351 other
Hyperdip-50-C26other0.006130.99387 other
Hyperdip-50-C27-Nother0.007280.99272 other
Hyperdip-50-C28other0.015590.98441 other
Hyperdip-50-C29other0.005490.99451 other
Hyperdip-50-C2other0.006160.99384 other
Hyperdip-50-C30other0.025830.97417 other
Hyperdip-50-C31other0.100110.89989 other
Hyperdip-50-C32other0.286790.71321 other
Hyperdip-50-C33 (testset)other0.001090.99891 other
Hyperdip-50-C34other0.198720.80128 other
Hyperdip-50-C35other0.051520.94848 other
Hyperdip-50-C36other0.074560.92544 other
Hyperdip-50-C37other0.035340.96466 other
Hyperdip-50-C38other0.086220.91378 other
Hyperdip-50-C39other0.016360.98364 other
Hyperdip-50-C3other0.003740.99626 other
Hyperdip-50-C40 (testset)other0.009780.99022 other
Hyperdip-50-C41other0.028330.97167 other
Hyperdip-50-C42 (testset)other0.083480.91652 other
Hyperdip-50-C43other0.003110.99689 other
Hyperdip-50-C4other0.024020.97598 other
Hyperdip-50-C5 (testset)other0.010920.98908 other
Hyperdip-50-C6other0.017840.98216 other
Hyperdip-50-C7other0.048940.95106 other
Hyperdip-50-C8 (testset)other0.040320.95968 other
Hyperdip-50-C9other0.012070.98793 other
Hyperdip-50-R1other0.049780.95022 other
Hyperdip-50-R2other0.007740.99226 other
Hyperdip-50-R3other0.001230.99877 other
Hyperdip-50-R4 (testset)other0.014250.98575 other
Hyperdip-50-R5 (testset)other0.013190.98681 other
Hyperdip47-50-1 (testset)other0.10290.8971 other
Hyperdip47-50-2 (testset)other0.056460.94354 other
Hyperdip47-50-3other0.01730.9827 other
Hyperdip47-50-2M1other0.188760.81124 other
Hyperdip47-50-C10 (testset)other0.028860.97114 other
Hyperdip47-50-C11other0.0080.992 other
Hyperdip47-50-C12other0.063420.93658 other
Hyperdip47-50-C13other0.00850.9915 other
Hyperdip47-50-C14-Nother0.011790.98821 other
Hyperdip47-50-C15other0.012260.98774 other
Hyperdip47-50-C16other0.002280.99772 other
Hyperdip47-50-C17 (testset)other0.034020.96598 other
Hyperdip47-50-C18 (testset)other0.035620.96438 other
Hyperdip47-50-C19other0.003880.99612 other
Hyperdip47-50-C1other0.002170.99783 other
Hyperdip47-50-C2 (testset)other0.01230.9877 other
Hyperdip47-50-C3-N (testset)other0.027490.97251 other
Hyperdip47-50-C4other0.002490.99751 other
Hyperdip47-50-C5other0.007640.99236 other
Hyperdip47-50-C6other0.10710.8929 other
Hyperdip47-50-C7other0.001940.99806 other
Hyperdip47-50-C8other0.028770.97123 other
Hyperdip47-50-C9other0.310840.68916 other
Hypodip-1other0.059840.94016 other
Hypodip-2 (testset)other0.011550.98845 other
Hypodip-2M1other0.061690.93831 other
Hypodip-C1 (testset)other0.075540.92446 other
Hypodip-C2other0.007860.99214 other
Hypodip-C3 (testset)other0.03130.9687 other
Hypodip-C4other0.021190.97881 other
Hypodip-C5other0.054380.94562 other
Hypodip-C6other0.030180.96982 other
MLL-1 (testset)other0.001950.99805 other
MLL-2 (testset)other0.001530.99847 other
MLL-3 (testset)other0.026950.97305 other
MLL-4other0.006040.99396 other
MLL-5other0.003350.99665 other
MLL-6 (testset)other0.023930.97607 other
MLL-7other0.008160.99184 other
MLL-8other0.006610.99339 other
MLL-2M1other0.002680.99732 other
MLL-2M2 (testset)other0.005860.99414 other
MLL-C1other0.012340.98766 other
MLL-C2other0.047860.95214 other
MLL-C3other0.018650.98135 other
MLL-C4 (testset)other0.007210.99279 other
MLL-C5other0.006530.99347 other
MLL-C6 (testset)other0.005320.99468 other
MLL-R1 (testset)other0.000870.99913 other
MLL-R2other0.004190.99581 other
MLL-R3other0.008920.99108 other
MLL-R4 (testset)other0.003590.99641 other
Normal-1other0.001360.99864 other
Normal-2 (testset)other0.158390.84161 other
Normal-3 (testset)other0.16840.8316 other
Normal-C1-Nother0.006420.99358 other
Normal-C10 (testset)other0.008360.99164 other
Normal-C11-Nother0.003390.99661 other
Normal-C12 (testset)other0.001070.99893 other
Normal-C2-N (testset)other0.012560.98744 other
Normal-C3-Nother0.002580.99742 other
Normal-C4-Nother0.018520.98148 other
Normal-C5 (testset)other0.027520.97248 other
Normal-C6 (testset)other0.009140.99086 other
Normal-C7-Nother0.003130.99687 other
Normal-C8 (testset)other0.053840.94616 other
Normal-C9 (testset)other0.048120.95188 other
Normal-R1other0.094520.90548 other
Normal-R2-Nother0.020590.97941 other
Normal-R3 (testset)other0.003670.99633 other
Pseudodip-1 (testset)other0.131470.86853 other
Pseudodip-2other0.029930.97007 other
Pseudodip-3 (testset)other0.05710.9429 other
Pseudodip-4other0.116770.88323 other
Pseudodip-5other0.120470.87953 other
Pseudodip-6other0.051070.94893 other
Pseudodip-7other0.106030.89397 other
Pseudodip-8-N (testset)other0.007520.99248 other
Pseudodip-9other0.113690.88631 other
Pseudodip-C10other0.051140.94886 other
Pseudodip-C11other0.22490.7751 other
Pseudodip-C12other0.043530.95647 other
Pseudodip-C13other0.019690.98031 other
Pseudodip-C14 (testset)other0.316620.68338 other
Pseudodip-C15other0.003990.99601 other
Pseudodip-C16-Nother0.019760.98024 other
Pseudodip-C17other0.018160.98184 other
Pseudodip-C18 (testset)other0.013910.98609 other
Pseudodip-C19other0.052550.94745 other
Pseudodip-C1other0.034890.96511 other
Pseudodip-C2-Nother0.00210.9979 other
Pseudodip-C3 (testset)other0.00370.9963 other
Pseudodip-C4other0.002630.99737 other
Pseudodip-C5 (testset)other0.011180.98882 other
Pseudodip-C6other0.048880.95112 other
Pseudodip-C7other0.143140.85686 other
Pseudodip-C8other0.013290.98671 other
Pseudodip-C9other0.03250.9675 other
Pseudodip-R1-N (testset)other0.012670.98733 other
T-ALL-10 (testset)other0.001140.99886 other
T-ALL-1other0.01180.9882 other
T-ALL-2other0.000620.99938 other
T-ALL-3 (testset)other0.197650.80235 other
T-ALL-4other0.007260.99274 other
T-ALL-5 (testset)other0.001240.99876 other
T-ALL-6other0.006150.99385 other
T-ALL-7other0.005170.99483 other
T-ALL-8other0.003480.99652 other
T-ALL-9 (testset)other0.058440.94156 other
T-ALL-2M1other0.026890.97311 other
T-ALL-C10other0.005110.99489 other
T-ALL-C11other0.193360.80664 other
T-ALL-C12 (testset)other0.009560.99044 other
T-ALL-C13 (testset)other0.010190.98981 other
T-ALL-C14 (testset)other0.002390.99761 other
T-ALL-C15other0.018110.98189 other
T-ALL-C16other0.001810.99819 other
T-ALL-C17other0.014660.98534 other
T-ALL-C18 (testset)other0.004950.99505 other
T-ALL-C19other0.046240.95376 other
T-ALL-C1other0.002840.99716 other
T-ALL-C20 (testset)other0.013540.98646 other
T-ALL-C21other0.044460.95554 other
T-ALL-C22 (testset)other0.006580.99342 other
T-ALL-C23other0.003340.99666 other
T-ALL-C24other0.001730.99827 other
T-ALL-C25other0.004480.99552 other
T-ALL-C26other0.002640.99736 other
T-ALL-C2other0.014460.98554 other
T-ALL-C3 (testset)other0.008880.99112 other
T-ALL-C4other0.004940.99506 other
T-ALL-C5other0.009760.99024 other
T-ALL-C6other0.007860.99214 other
T-ALL-C7 (testset)other0.005470.99453 other
T-ALL-C8other0.001980.99802 other
T-ALL-C9other0.016620.98338 other
T-ALL-R1other0.001740.99826 other
T-ALL-R2 (testset)other0.229420.77058 other
T-ALL-R3other0.002870.99713 other
T-ALL-R4other0.00440.9956 other
T-ALL-R5 (testset)other0.127330.87267 other
T-ALL-R6other0.04860.9514 other
TEL-AML1-10other0.06650.9335 other
TEL-AML1-11other0.007530.99247 other
TEL-AML1-12 (testset)other0.007940.99206 other
TEL-AML1-13other0.012380.98762 other
TEL-AML1-14other0.012130.98787 other
TEL-AML1-1 (testset)other0.002990.99701 other
TEL-AML1-2other0.008490.99151 other
TEL-AML1-3other0.02590.9741 other
TEL-AML1-4other0.009730.99027 other
TEL-AML1-5 (testset)other0.003620.99638 other
TEL-AML1-6other0.001150.99885 other
TEL-AML1-7 (testset)other0.016120.98388 other
TEL-AML1-8other0.002760.99724 other
TEL-AML1-9 (testset)other0.031920.96808 other
TEL-AML1-2M1 (testset)other0.126780.87322 other
TEL-AML1-2M2other0.010070.98993 other
TEL-AML1-2M3 (testset)other0.007580.99242 other
TEL-AML1-2M4 (testset)other0.011790.98821 other
TEL-AML1-2M5other0.007730.99227 other
TEL-AML1-C10other0.017330.98267 other
TEL-AML1-C11other0.061520.93848 other
TEL-AML1-C12other0.003310.99669 other
TEL-AML1-C13other0.014770.98523 other
TEL-AML1-C14other0.01650.9835 other
TEL-AML1-C15 (testset)other0.038720.96128 other
TEL-AML1-C16 (testset)other0.13240.8676 other
TEL-AML1-C17 (testset)other0.002740.99726 other
TEL-AML1-C18other0.033160.96684 other
TEL-AML1-C19 (testset)other0.008520.99148 other
TEL-AML1-C1other0.007980.99202 other
TEL-AML1-C20other0.016120.98388 other
TEL-AML1-C21other0.008950.99105 other
TEL-AML1-C22other0.007680.99232 other
TEL-AML1-C23other0.002750.99725 other
TEL-AML1-C24other0.053350.94665 other
TEL-AML1-C25 (testset)other0.008430.99157 other
TEL-AML1-C26 (testset)other0.031030.96897 other
TEL-AML1-C27other0.006110.99389 other
TEL-AML1-C28other0.025910.97409 other
TEL-AML1-C29other0.014670.98533 other
TEL-AML1-C2other0.008110.99189 other
TEL-AML1-C30other0.028270.97173 other
TEL-AML1-C31 (testset)other0.038620.96138 other
TEL-AML1-C32 (testset)other0.031050.96895 other
TEL-AML1-C33other0.004570.99543 other
TEL-AML1-C34 (testset)other0.019180.98082 other
TEL-AML1-C35 (testset)other0.04510.9549 other
TEL-AML1-C36 (testset)other0.008090.99191 other
TEL-AML1-C37other0.022850.97715 other
TEL-AML1-C38 (testset)other0.064560.93544 other
TEL-AML1-C39 (testset)other0.00670.9933 other
TEL-AML1-C3 (testset)other0.010820.98918 other
TEL-AML1-C40other0.006880.99312 other
TEL-AML1-C41other0.006220.99378 other
TEL-AML1-C42other0.008430.99157 other
TEL-AML1-C43other0.006710.99329 other
TEL-AML1-C44other0.016370.98363 other
TEL-AML1-C45other0.003840.99616 other
TEL-AML1-C46other0.006740.99326 other
TEL-AML1-C47other0.005930.99407 other
TEL-AML1-C48other0.117740.88226 other
TEL-AML1-C49 (testset)other0.009890.99011 other
TEL-AML1-C4 (testset)other0.007540.99246 other
TEL-AML1-C50other0.0060.994 other
TEL-AML1-C51other0.042690.95731 other
TEL-AML1-C52 (testset)other0.088850.91115 other
TEL-AML1-C53other0.069320.93068 other
TEL-AML1-C54 (testset)other0.011710.98829 other
TEL-AML1-C55other0.003970.99603 other
TEL-AML1-C56other0.007770.99223 other
TEL-AML1-C57 (testset)other0.010570.98943 other
TEL-AML1-C5other0.025110.97489 other
TEL-AML1-C6other0.004140.99586 other
TEL-AML1-C7other0.008580.99142 other
TEL-AML1-C8other0.001410.99859 other
TEL-AML1-C9 (testset)other0.005360.99464 other
TEL-AML1-R1other0.006460.99354 other
TEL-AML1-R2 (testset)other0.146720.85328 other
TEL-AML1-R3 (testset)other0.012860.98714 other

 


Generated by StAM on Tue Sep 7 18:20:25 2004