StAM Report: Prediction of MLL (predictive) - beta 0.06, 0.94



Information on Evaluation

Total number of samples: 327
Training samples: 217 ( 13 from MLL, 204 from other )
Test samples: 110 ( 7 from MLL, 103 from other )
Focus on class: MLL
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: 217
Number of classes: 2
Class weights: 'MLL': 0.06 'other': 0.94
Class prior: 'MLL':0.06 'other':0.94
Shrinkage candidates: 0, 0.015, 0.03, 0.045, 0.06, 0.075, 0.091, 0.106, 0.121, 0.136, 0.151, 0.166, 0.181, 0.196, 0.211, 0.226, 0.241, 0.256, 0.272, 0.287, 0.302, 0.317, 0.332, 0.347, 0.362, 0.377, 0.392, 0.407, 0.422, 0.437


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
000.114583.144922206779
0.01500.113773.147552206779
0.0300.112853.150722206779
0.04500.111783.154642206779
0.0600.110533.158692206779
0.07500.109063.161462206779
0.09100.107423.198482156779
0.10600.105813.212562136775
0.12100.104153.217262126719
0.13600.102243.258772056694
0.15100.100163.288391936630
0.16600.098013.483411686577
0.18100.095893.51571616461
0.19600.093883.602371506346
0.21100.091643.703121376269
0.22600.088933.762191286032
0.24100.085564.093541055607
0.25600.080894.52729865254
0.27200.076934.63085835222
0.28700.074354.91914724996
0.30200.072585.21736634705
0.31700.068985.70318533933
0.33200.064336.38122463011
0.34700.059496.73718432730
0.36200.056476.62239382534
0.37700.055699.44893272462
0.39200.0520511.88199211861
0.40700.0309316.65546151687
0.42200.0182426.0678791136


Information on Model Fit


Fit for D = 0.256

Number of classes: 2
Class weights: 'MLL': 0.06 'other': 0.94
Class prior: 'MLL':0.06 'other':0.94
Chosen shrinkage level: 0.256
(by the user )
Number of nodes left 86
Number of accessible genes 5254

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 (20 from MLL, 307 from other)
Test samples: 110 (7 from MLL, 103 from other)
Classes: MLL, 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
MLL0.923081
other10.92308

Performance on test data

 SensitivitySpecificity
MLL11
other11

Predictions

 ClassMLLotherPredictionn
BCR-ABL-1 (testset)other0.202590.79741 other
BCR-ABL-2 (testset)other0.004330.99567 other
BCR-ABL-3other0.0040.996 other
BCR-ABL-4other0.004190.99581 other
BCR-ABL-5 (testset)other0.002740.99726 other
BCR-ABL-6other0.08080.9192 other
BCR-ABL-7 (testset)other0.006090.99391 other
BCR-ABL-8 (testset)other0.020590.97941 other
BCR-ABL-9other0.00280.9972 other
BCR-ABL-C1 (testset)other0.041560.95844 other
BCR-ABL-Hyperdip-10other0.000350.99965 other
BCR-ABL-Hyperdip-R5other0.000710.99929 other
BCR-ABL-R1 (testset)other0.052770.94723 other
BCR-ABL-R2 (testset)other0.049230.95077 other
BCR-ABL-R3 (testset)other0.004960.99504 other
E2A-PBX1-10other0.041950.95805 other
E2A-PBX1-11other0.048770.95123 other
E2A-PBX1-12 (testset)other0.110360.88964 other
E2A-PBX1-13 (testset)other0.035290.96471 other
E2A-PBX1-1other0.094410.90559 other
E2A-PBX1-2other0.015060.98494 other
E2A-PBX1-3other0.023010.97699 other
E2A-PBX1-4other0.011010.98899 other
E2A-PBX1-5other0.030390.96961 other
E2A-PBX1-6 (testset)other0.1120.888 other
E2A-PBX1-7 (testset)other0.043320.95668 other
E2A-PBX1-8 (testset)other0.016380.98362 other
E2A-PBX1-9other0.021250.97875 other
E2A-PBX1-2M1other0.027340.97266 other
E2A-PBX1-C10 (testset)other0.025880.97412 other
E2A-PBX1-C11other0.09410.9059 other
E2A-PBX1-C12other0.028570.97143 other
E2A-PBX1-C1other0.022380.97762 other
E2A-PBX1-C2 (testset)other0.017050.98295 other
E2A-PBX1-C3other0.066380.93362 other
E2A-PBX1-C4other0.016110.98389 other
E2A-PBX1-C5other0.138510.86149 other
E2A-PBX1-C6other0.040230.95977 other
E2A-PBX1-C7other0.057290.94271 other
E2A-PBX1-C8 (testset)other0.057520.94248 other
E2A-PBX1-C9other0.045570.95443 other
E2A-PBX1-R1 (testset)other0.024420.97558 other
Hyperdip-50-10other0.000860.99914 other
Hyperdip-50-11other0.004180.99582 other
Hyperdip-50-12other0.001740.99826 other
Hyperdip-50-13other0.002320.99768 other
Hyperdip-50-14other0.001810.99819 other
Hyperdip-50-1other0.003780.99622 other
Hyperdip-50-2other0.000550.99945 other
Hyperdip-50-3other0.001190.99881 other
Hyperdip-50-4other0.013040.98696 other
Hyperdip-50-5other0.002830.99717 other
Hyperdip-50-6other0.002060.99794 other
Hyperdip-50-7 (testset)other0.020480.97952 other
Hyperdip-50-8other0.005610.99439 other
Hyperdip-50-9 (testset)other0.002650.99735 other
Hyperdip-50-2M1other0.000940.99906 other
Hyperdip-50-2M2 (testset)other0.008450.99155 other
Hyperdip-50-C10 (testset)other0.002340.99766 other
Hyperdip-50-C11other0.003960.99604 other
Hyperdip-50-C12other0.003930.99607 other
Hyperdip-50-C13other0.001080.99892 other
Hyperdip-50-C14other0.001860.99814 other
Hyperdip-50-C15other0.003360.99664 other
Hyperdip-50-C16other0.005490.99451 other
Hyperdip-50-C17other0.002530.99747 other
Hyperdip-50-C18 (testset)other0.001890.99811 other
Hyperdip-50-C19other0.015390.98461 other
Hyperdip-50-C1 (testset)other0.006160.99384 other
Hyperdip-50-C20other0.001060.99894 other
Hyperdip-50-C21other0.000970.99903 other
Hyperdip-50-C22other0.002120.99788 other
Hyperdip-50-C23 (testset)other0.001240.99876 other
Hyperdip-50-C24other0.001530.99847 other
Hyperdip-50-C25 (testset)other0.002350.99765 other
Hyperdip-50-C26 (testset)other0.002210.99779 other
Hyperdip-50-C27-Nother0.008430.99157 other
Hyperdip-50-C28other0.02630.9737 other
Hyperdip-50-C29other0.003760.99624 other
Hyperdip-50-C2other0.002840.99716 other
Hyperdip-50-C30 (testset)other0.009650.99035 other
Hyperdip-50-C31 (testset)other0.001620.99838 other
Hyperdip-50-C32other0.023370.97663 other
Hyperdip-50-C33other0.003810.99619 other
Hyperdip-50-C34other0.000560.99944 other
Hyperdip-50-C35other0.000990.99901 other
Hyperdip-50-C36 (testset)other0.000920.99908 other
Hyperdip-50-C37other0.001390.99861 other
Hyperdip-50-C38other0.000390.99961 other
Hyperdip-50-C39other0.000580.99942 other
Hyperdip-50-C3 (testset)other0.006910.99309 other
Hyperdip-50-C40 (testset)other0.001550.99845 other
Hyperdip-50-C41other4e-040.9996 other
Hyperdip-50-C42 (testset)other2e-040.9998 other
Hyperdip-50-C43 (testset)other0.015650.98435 other
Hyperdip-50-C4other0.001740.99826 other
Hyperdip-50-C5other0.001930.99807 other
Hyperdip-50-C6 (testset)other0.001890.99811 other
Hyperdip-50-C7other0.002710.99729 other
Hyperdip-50-C8other0.002880.99712 other
Hyperdip-50-C9other0.001860.99814 other
Hyperdip-50-R1 (testset)other0.000650.99935 other
Hyperdip-50-R2other0.003240.99676 other
Hyperdip-50-R3 (testset)other0.048730.95127 other
Hyperdip-50-R4other0.001240.99876 other
Hyperdip-50-R5 (testset)other0.002230.99777 other
Hyperdip47-50-1other0.007270.99273 other
Hyperdip47-50-2other0.005760.99424 other
Hyperdip47-50-3other0.25360.7464 other
Hyperdip47-50-2M1other0.002920.99708 other
Hyperdip47-50-C10 (testset)other0.006780.99322 other
Hyperdip47-50-C11other0.004440.99556 other
Hyperdip47-50-C12other0.011110.98889 other
Hyperdip47-50-C13other0.07710.9229 other
Hyperdip47-50-C14-Nother0.012530.98747 other
Hyperdip47-50-C15other0.002750.99725 other
Hyperdip47-50-C16 (testset)other0.447270.55273 other
Hyperdip47-50-C17other0.002820.99718 other
Hyperdip47-50-C18other0.097210.90279 other
Hyperdip47-50-C19other0.015470.98453 other
Hyperdip47-50-C1 (testset)other0.13090.8691 other
Hyperdip47-50-C2other0.021620.97838 other
Hyperdip47-50-C3-Nother0.021220.97878 other
Hyperdip47-50-C4other0.007780.99222 other
Hyperdip47-50-C5other0.137230.86277 other
Hyperdip47-50-C6other0.00520.9948 other
Hyperdip47-50-C7other0.028020.97198 other
Hyperdip47-50-C8other0.008570.99143 other
Hyperdip47-50-C9other0.009840.99016 other
Hypodip-1other0.016210.98379 other
Hypodip-2other0.009940.99006 other
Hypodip-2M1 (testset)other0.012070.98793 other
Hypodip-C1 (testset)other0.004960.99504 other
Hypodip-C2other0.010020.98998 other
Hypodip-C3other0.010650.98935 other
Hypodip-C4other0.43930.5607 other
Hypodip-C5 (testset)other0.002180.99782 other
Hypodip-C6 (testset)other0.021540.97846 other
MLL-1MLL0.813530.18647 MLL
MLL-2 (testset)MLL0.643140.35686 MLL
MLL-3 (testset)MLL0.909470.09053 MLL
MLL-4MLL0.936040.06396 MLL
MLL-5 (testset)MLL0.779110.22089 MLL
MLL-6 (testset)MLL0.620360.37964 MLL
MLL-7MLL0.585780.41422 MLL
MLL-8MLL0.631930.36807 MLL
MLL-2M1 (testset)MLL0.635970.36403 MLL
MLL-2M2MLL0.942920.05708 MLL
MLL-C1MLL0.94690.0531 MLL
MLL-C2 (testset)MLL0.872470.12753 MLL
MLL-C3MLL0.829960.17004 MLL
MLL-C4MLL0.68820.3118 MLL
MLL-C5MLL0.804530.19547 MLL
MLL-C6MLL0.724010.27599 MLL
MLL-R1MLL0.61530.3847 MLL
MLL-R2MLL0.804910.19509 MLL
MLL-R3MLL0.958120.04188 MLL
MLL-R4 (testset)MLL0.607350.39265 MLL
Normal-1other0.065240.93476 other
Normal-2other0.032530.96747 other
Normal-3other0.005970.99403 other
Normal-C1-N (testset)other0.010390.98961 other
Normal-C10 (testset)other0.098710.90129 other
Normal-C11-Nother0.029110.97089 other
Normal-C12other0.014860.98514 other
Normal-C2-Nother0.012570.98743 other
Normal-C3-Nother0.025280.97472 other
Normal-C4-Nother0.022490.97751 other
Normal-C5 (testset)other0.013480.98652 other
Normal-C6 (testset)other0.038140.96186 other
Normal-C7-Nother0.021410.97859 other
Normal-C8other0.042860.95714 other
Normal-C9other0.006030.99397 other
Normal-R1 (testset)other0.099410.90059 other
Normal-R2-Nother0.009350.99065 other
Normal-R3other0.020360.97964 other
Pseudodip-1other0.007310.99269 other
Pseudodip-2 (testset)other0.001130.99887 other
Pseudodip-3other0.01050.9895 other
Pseudodip-4other0.004040.99596 other
Pseudodip-5other0.023990.97601 other
Pseudodip-6other0.01120.9888 other
Pseudodip-7other0.019410.98059 other
Pseudodip-8-Nother0.030660.96934 other
Pseudodip-9 (testset)other0.008060.99194 other
Pseudodip-C10other0.009340.99066 other
Pseudodip-C11other0.002790.99721 other
Pseudodip-C12other0.001970.99803 other
Pseudodip-C13other0.010860.98914 other
Pseudodip-C14other0.026710.97329 other
Pseudodip-C15other0.004370.99563 other
Pseudodip-C16-N (testset)other0.00650.9935 other
Pseudodip-C17other0.001750.99825 other
Pseudodip-C18other0.029840.97016 other
Pseudodip-C19other0.009820.99018 other
Pseudodip-C1other0.025210.97479 other
Pseudodip-C2-Nother0.015750.98425 other
Pseudodip-C3other0.021330.97867 other
Pseudodip-C4 (testset)other0.031210.96879 other
Pseudodip-C5other0.039170.96083 other
Pseudodip-C6other0.010660.98934 other
Pseudodip-C7other0.04580.9542 other
Pseudodip-C8other0.066720.93328 other
Pseudodip-C9other0.026530.97347 other
Pseudodip-R1-N (testset)other0.004220.99578 other
T-ALL-10other0.020040.97996 other
T-ALL-1other0.076830.92317 other
T-ALL-2other0.14760.8524 other
T-ALL-3 (testset)other0.010670.98933 other
T-ALL-4 (testset)other0.008850.99115 other
T-ALL-5 (testset)other0.01830.9817 other
T-ALL-6 (testset)other0.004560.99544 other
T-ALL-7other0.030690.96931 other
T-ALL-8other0.021420.97858 other
T-ALL-9other0.034270.96573 other
T-ALL-2M1 (testset)other0.038730.96127 other
T-ALL-C10other0.009390.99061 other
T-ALL-C11other0.003980.99602 other
T-ALL-C12other0.021430.97857 other
T-ALL-C13other0.007620.99238 other
T-ALL-C14 (testset)other0.020650.97935 other
T-ALL-C15other0.014440.98556 other
T-ALL-C16 (testset)other0.057920.94208 other
T-ALL-C17 (testset)other0.039950.96005 other
T-ALL-C18other0.170050.82995 other
T-ALL-C19other0.008020.99198 other
T-ALL-C1 (testset)other0.026920.97308 other
T-ALL-C20other0.021440.97856 other
T-ALL-C21 (testset)other0.006090.99391 other
T-ALL-C22other0.008010.99199 other
T-ALL-C23other0.00410.9959 other
T-ALL-C24 (testset)other0.027080.97292 other
T-ALL-C25other0.013190.98681 other
T-ALL-C26other0.023430.97657 other
T-ALL-C2other0.017770.98223 other
T-ALL-C3 (testset)other0.007670.99233 other
T-ALL-C4other0.015790.98421 other
T-ALL-C5other0.069910.93009 other
T-ALL-C6other0.02980.9702 other
T-ALL-C7other0.011040.98896 other
T-ALL-C8other0.021260.97874 other
T-ALL-C9other0.014730.98527 other
T-ALL-R1 (testset)other0.007310.99269 other
T-ALL-R2other0.01950.9805 other
T-ALL-R3other0.008170.99183 other
T-ALL-R4other0.003170.99683 other
T-ALL-R5 (testset)other0.091850.90815 other
T-ALL-R6 (testset)other0.090680.90932 other
TEL-AML1-10other0.001460.99854 other
TEL-AML1-11 (testset)other0.007750.99225 other
TEL-AML1-12other0.006560.99344 other
TEL-AML1-13other0.013450.98655 other
TEL-AML1-14other0.00150.9985 other
TEL-AML1-1other0.002730.99727 other
TEL-AML1-2 (testset)other0.002160.99784 other
TEL-AML1-3other0.001990.99801 other
TEL-AML1-4 (testset)other0.001270.99873 other
TEL-AML1-5 (testset)other0.006380.99362 other
TEL-AML1-6 (testset)other0.044990.95501 other
TEL-AML1-7other0.00630.9937 other
TEL-AML1-8 (testset)other0.003730.99627 other
TEL-AML1-9 (testset)other0.00410.9959 other
TEL-AML1-2M1other0.004620.99538 other
TEL-AML1-2M2 (testset)other0.003720.99628 other
TEL-AML1-2M3other0.001360.99864 other
TEL-AML1-2M4other0.001930.99807 other
TEL-AML1-2M5other0.001350.99865 other
TEL-AML1-C10 (testset)other0.002360.99764 other
TEL-AML1-C11 (testset)other0.00330.9967 other
TEL-AML1-C12 (testset)other0.00210.9979 other
TEL-AML1-C13 (testset)other0.002980.99702 other
TEL-AML1-C14other0.004370.99563 other
TEL-AML1-C15other0.004480.99552 other
TEL-AML1-C16other0.011340.98866 other
TEL-AML1-C17other0.008690.99131 other
TEL-AML1-C18other0.00570.9943 other
TEL-AML1-C19other0.003020.99698 other
TEL-AML1-C1other0.005980.99402 other
TEL-AML1-C20other0.002110.99789 other
TEL-AML1-C21 (testset)other0.016690.98331 other
TEL-AML1-C22 (testset)other0.001230.99877 other
TEL-AML1-C23other0.013290.98671 other
TEL-AML1-C24other0.004530.99547 other
TEL-AML1-C25other0.007430.99257 other
TEL-AML1-C26 (testset)other0.006330.99367 other
TEL-AML1-C27other0.002930.99707 other
TEL-AML1-C28 (testset)other0.025840.97416 other
TEL-AML1-C29other0.001020.99898 other
TEL-AML1-C2other0.00280.9972 other
TEL-AML1-C30 (testset)other0.004160.99584 other
TEL-AML1-C31 (testset)other0.003760.99624 other
TEL-AML1-C32other0.000520.99948 other
TEL-AML1-C33other0.002770.99723 other
TEL-AML1-C34 (testset)other0.000780.99922 other
TEL-AML1-C35 (testset)other0.006670.99333 other
TEL-AML1-C36other0.002520.99748 other
TEL-AML1-C37 (testset)other0.001310.99869 other
TEL-AML1-C38other0.001540.99846 other
TEL-AML1-C39other0.003340.99666 other
TEL-AML1-C3other0.004270.99573 other
TEL-AML1-C40 (testset)other0.005060.99494 other
TEL-AML1-C41other0.00340.9966 other
TEL-AML1-C42 (testset)other0.002910.99709 other
TEL-AML1-C43other0.00240.9976 other
TEL-AML1-C44other0.008070.99193 other
TEL-AML1-C45other0.010550.98945 other
TEL-AML1-C46 (testset)other0.002660.99734 other
TEL-AML1-C47other0.001060.99894 other
TEL-AML1-C48other0.003060.99694 other
TEL-AML1-C49 (testset)other0.003240.99676 other
TEL-AML1-C4 (testset)other0.006850.99315 other
TEL-AML1-C50 (testset)other0.003980.99602 other
TEL-AML1-C51other0.000770.99923 other
TEL-AML1-C52other0.002050.99795 other
TEL-AML1-C53 (testset)other0.009650.99035 other
TEL-AML1-C54 (testset)other0.001310.99869 other
TEL-AML1-C55other0.003290.99671 other
TEL-AML1-C56 (testset)other0.004840.99516 other
TEL-AML1-C57other0.001350.99865 other
TEL-AML1-C5other0.003590.99641 other
TEL-AML1-C6 (testset)other0.002670.99733 other
TEL-AML1-C7 (testset)other0.002330.99767 other
TEL-AML1-C8other0.009430.99057 other
TEL-AML1-C9other0.009880.99012 other
TEL-AML1-R1 (testset)other0.003910.99609 other
TEL-AML1-R2other0.003280.99672 other
TEL-AML1-R3other0.003060.99694 other

 


Generated by StAM on Wed Sep 8 11:56:20 2004