StAM Report: Prediction of T-ALL (predictive) - beta 0.133, 0.867



Information on Evaluation

Total number of samples: 327
Training samples: 218 ( 29 from T-ALL, 189 from other )
Test samples: 109 ( 14 from T-ALL, 95 from other )
Focus on class: T-ALL
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: 'T-ALL': 0.133 'other': 0.867
Class prior: 'T-ALL':0.133 'other':0.867
Shrinkage candidates: 0, 0.027, 0.054, 0.081, 0.108, 0.135, 0.162, 0.189, 0.216, 0.243, 0.27, 0.297, 0.324, 0.352, 0.379, 0.406, 0.433, 0.46, 0.487, 0.514, 0.541, 0.568, 0.595, 0.622, 0.649, 0.676, 0.703, 0.73, 0.757, 0.784


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
000.231891.984417418189
0.02700.223171.990037418189
0.05400.213772.016287228183
0.08100.205862.039247058139
0.10800.197532.08036738070
0.13500.189362.133976288027
0.16200.181012.210865727972
0.18900.171132.264785397955
0.21600.160562.31475077777
0.24300.150912.422564517662
0.2700.141052.514694127526
0.29700.13162.626043657448
0.32400.122372.759073247371
0.35200.114062.856423017302
0.37900.107472.976662787161
0.40600.101893.11842517105
0.43300.097883.215772377052
0.4600.093313.220162267007
0.48700.088793.393482056946
0.51400.08413.421931956909
0.54100.078963.580081706461
0.56800.073553.895241496298
0.59500.067294.243721335967
0.62200.060684.623921185124
0.64900.050454.95373984846
0.67600.032856.03003774459
0.70300.02686.75656704274
0.7300.020698.39954513845
0.75700.012899.05536313270


Information on Model Fit


Fit for D = 0.649

Number of classes: 2
Class weights: 'T-ALL': 0.133 'other': 0.867
Class prior: 'T-ALL':0.133 'other':0.867
Chosen shrinkage level: 0.649
(by optimizing the root's error rate )
Number of nodes left 98
Number of accessible genes 4846

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 (43 from T-ALL, 284 from other)
Test samples: 109 (14 from T-ALL, 95 from other)
Classes: T-ALL, 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
T-ALL11
other11

Performance on test data

 SensitivitySpecificity
T-ALL0.928571
other10.92857

Predictions

 ClassT-ALLotherPredictionn
BCR-ABL-1other0.042180.95782 other
BCR-ABL-2other0.011460.98854 other
BCR-ABL-3 (testset)other0.003260.99674 other
BCR-ABL-4other0.003590.99641 other
BCR-ABL-5other0.004420.99558 other
BCR-ABL-6 (testset)other0.009410.99059 other
BCR-ABL-7 (testset)other0.014130.98587 other
BCR-ABL-8 (testset)other0.002960.99704 other
BCR-ABL-9 (testset)other0.003120.99688 other
BCR-ABL-C1 (testset)other0.008930.99107 other
BCR-ABL-Hyperdip-10 (testset)other0.003160.99684 other
BCR-ABL-Hyperdip-R5other0.00330.9967 other
BCR-ABL-R1other0.014040.98596 other
BCR-ABL-R2other0.031850.96815 other
BCR-ABL-R3 (testset)other0.013540.98646 other
E2A-PBX1-10other0.004280.99572 other
E2A-PBX1-11other0.005040.99496 other
E2A-PBX1-12 (testset)other0.005680.99432 other
E2A-PBX1-13other0.010450.98955 other
E2A-PBX1-1other0.003880.99612 other
E2A-PBX1-2other0.012710.98729 other
E2A-PBX1-3other0.006010.99399 other
E2A-PBX1-4 (testset)other0.004570.99543 other
E2A-PBX1-5other0.003810.99619 other
E2A-PBX1-6other0.003770.99623 other
E2A-PBX1-7other0.006510.99349 other
E2A-PBX1-8other0.007230.99277 other
E2A-PBX1-9other0.011580.98842 other
E2A-PBX1-2M1other0.01030.9897 other
E2A-PBX1-C10other0.011720.98828 other
E2A-PBX1-C11other0.014950.98505 other
E2A-PBX1-C12other0.007190.99281 other
E2A-PBX1-C1other0.021410.97859 other
E2A-PBX1-C2other0.005170.99483 other
E2A-PBX1-C3 (testset)other0.004150.99585 other
E2A-PBX1-C4other0.006170.99383 other
E2A-PBX1-C5 (testset)other0.008980.99102 other
E2A-PBX1-C6other0.004660.99534 other
E2A-PBX1-C7other0.003740.99626 other
E2A-PBX1-C8other0.081460.91854 other
E2A-PBX1-C9other0.005750.99425 other
E2A-PBX1-R1other0.004730.99527 other
Hyperdip-50-10other0.008930.99107 other
Hyperdip-50-11 (testset)other0.031940.96806 other
Hyperdip-50-12other0.007180.99282 other
Hyperdip-50-13 (testset)other0.008290.99171 other
Hyperdip-50-14other0.003210.99679 other
Hyperdip-50-1other0.004630.99537 other
Hyperdip-50-2other0.007250.99275 other
Hyperdip-50-3 (testset)other0.005010.99499 other
Hyperdip-50-4 (testset)other0.091550.90845 other
Hyperdip-50-5 (testset)other0.002980.99702 other
Hyperdip-50-6other0.005260.99474 other
Hyperdip-50-7other0.011960.98804 other
Hyperdip-50-8 (testset)other0.003130.99687 other
Hyperdip-50-9other0.006930.99307 other
Hyperdip-50-2M1other0.007990.99201 other
Hyperdip-50-2M2 (testset)other0.013160.98684 other
Hyperdip-50-C10other0.005310.99469 other
Hyperdip-50-C11 (testset)other0.003530.99647 other
Hyperdip-50-C12other0.005090.99491 other
Hyperdip-50-C13other0.006660.99334 other
Hyperdip-50-C14other0.004290.99571 other
Hyperdip-50-C15other0.004750.99525 other
Hyperdip-50-C16other0.00470.9953 other
Hyperdip-50-C17other0.007870.99213 other
Hyperdip-50-C18other0.005210.99479 other
Hyperdip-50-C19 (testset)other0.005830.99417 other
Hyperdip-50-C1other0.004440.99556 other
Hyperdip-50-C20other0.004760.99524 other
Hyperdip-50-C21other0.013420.98658 other
Hyperdip-50-C22 (testset)other0.003590.99641 other
Hyperdip-50-C23other0.00250.9975 other
Hyperdip-50-C24other0.006550.99345 other
Hyperdip-50-C25other0.005280.99472 other
Hyperdip-50-C26other0.004720.99528 other
Hyperdip-50-C27-Nother0.008080.99192 other
Hyperdip-50-C28other0.005930.99407 other
Hyperdip-50-C29 (testset)other0.010480.98952 other
Hyperdip-50-C2 (testset)other0.022390.97761 other
Hyperdip-50-C30other0.003890.99611 other
Hyperdip-50-C31other0.003090.99691 other
Hyperdip-50-C32other0.002780.99722 other
Hyperdip-50-C33other0.004910.99509 other
Hyperdip-50-C34other0.008450.99155 other
Hyperdip-50-C35 (testset)other0.012590.98741 other
Hyperdip-50-C36other0.006450.99355 other
Hyperdip-50-C37other0.004740.99526 other
Hyperdip-50-C38other0.006740.99326 other
Hyperdip-50-C39 (testset)other0.006410.99359 other
Hyperdip-50-C3other0.004570.99543 other
Hyperdip-50-C40other0.005530.99447 other
Hyperdip-50-C41 (testset)other0.00840.9916 other
Hyperdip-50-C42 (testset)other0.007170.99283 other
Hyperdip-50-C43other0.007340.99266 other
Hyperdip-50-C4other0.005790.99421 other
Hyperdip-50-C5 (testset)other0.016670.98333 other
Hyperdip-50-C6other0.006930.99307 other
Hyperdip-50-C7 (testset)other0.003760.99624 other
Hyperdip-50-C8 (testset)other0.002980.99702 other
Hyperdip-50-C9other0.003740.99626 other
Hyperdip-50-R1other0.012740.98726 other
Hyperdip-50-R2 (testset)other0.004810.99519 other
Hyperdip-50-R3other0.083050.91695 other
Hyperdip-50-R4other0.006160.99384 other
Hyperdip-50-R5 (testset)other0.00540.9946 other
Hyperdip47-50-1other0.005670.99433 other
Hyperdip47-50-2other0.00540.9946 other
Hyperdip47-50-3 (testset)other0.255260.74474 other
Hyperdip47-50-2M1 (testset)other0.002990.99701 other
Hyperdip47-50-C10 (testset)other0.004820.99518 other
Hyperdip47-50-C11other0.009860.99014 other
Hyperdip47-50-C12other0.01980.9802 other
Hyperdip47-50-C13other0.036530.96347 other
Hyperdip47-50-C14-N (testset)other0.026950.97305 other
Hyperdip47-50-C15 (testset)other0.003170.99683 other
Hyperdip47-50-C16other0.005690.99431 other
Hyperdip47-50-C17other0.003820.99618 other
Hyperdip47-50-C18other0.004640.99536 other
Hyperdip47-50-C19other0.078670.92133 other
Hyperdip47-50-C1 (testset)other0.036960.96304 other
Hyperdip47-50-C2 (testset)other0.01350.9865 other
Hyperdip47-50-C3-N (testset)other0.039620.96038 other
Hyperdip47-50-C4other0.006460.99354 other
Hyperdip47-50-C5 (testset)other0.128290.87171 other
Hyperdip47-50-C6 (testset)other0.011750.98825 other
Hyperdip47-50-C7other0.027130.97287 other
Hyperdip47-50-C8other0.006440.99356 other
Hyperdip47-50-C9other0.00230.9977 other
Hypodip-1 (testset)other0.004650.99535 other
Hypodip-2other0.044960.95504 other
Hypodip-2M1 (testset)other0.015840.98416 other
Hypodip-C1other0.006450.99355 other
Hypodip-C2 (testset)other0.012640.98736 other
Hypodip-C3other0.01350.9865 other
Hypodip-C4other0.022850.97715 other
Hypodip-C5other0.003480.99652 other
Hypodip-C6 (testset)other0.012050.98795 other
MLL-1 (testset)other0.093420.90658 other
MLL-2other0.183030.81697 other
MLL-3 (testset)other0.114380.88562 other
MLL-4other0.023780.97622 other
MLL-5 (testset)other0.005440.99456 other
MLL-6 (testset)other0.161850.83815 other
MLL-7other0.004080.99592 other
MLL-8 (testset)other0.008110.99189 other
MLL-2M1other0.062440.93756 other
MLL-2M2 (testset)other0.007990.99201 other
MLL-C1other0.008960.99104 other
MLL-C2other0.022350.97765 other
MLL-C3 (testset)other0.033330.96667 other
MLL-C4other0.013240.98676 other
MLL-C5other0.014550.98545 other
MLL-C6other0.010270.98973 other
MLL-R1 (testset)other0.168810.83119 other
MLL-R2other0.00680.9932 other
MLL-R3other0.039130.96087 other
MLL-R4other0.011850.98815 other
Normal-1other0.005170.99483 other
Normal-2other0.006960.99304 other
Normal-3other0.003670.99633 other
Normal-C1-Nother0.01120.9888 other
Normal-C10other0.019740.98026 other
Normal-C11-N (testset)other0.011840.98816 other
Normal-C12 (testset)other0.037410.96259 other
Normal-C2-Nother0.013550.98645 other
Normal-C3-Nother0.0570.943 other
Normal-C4-Nother0.025850.97415 other
Normal-C5other0.02490.9751 other
Normal-C6 (testset)other0.005170.99483 other
Normal-C7-N (testset)other0.022580.97742 other
Normal-C8other0.005270.99473 other
Normal-C9 (testset)other0.004020.99598 other
Normal-R1 (testset)other0.011090.98891 other
Normal-R2-Nother0.011580.98842 other
Normal-R3other0.018040.98196 other
Pseudodip-1other0.004350.99565 other
Pseudodip-2other0.021870.97813 other
Pseudodip-3other0.012450.98755 other
Pseudodip-4 (testset)other0.009710.99029 other
Pseudodip-5 (testset)other0.004980.99502 other
Pseudodip-6 (testset)other0.003240.99676 other
Pseudodip-7other0.005290.99471 other
Pseudodip-8-Nother0.018930.98107 other
Pseudodip-9other0.009540.99046 other
Pseudodip-C10 (testset)other0.0080.992 other
Pseudodip-C11 (testset)other0.0240.976 other
Pseudodip-C12 (testset)other0.013720.98628 other
Pseudodip-C13other0.007740.99226 other
Pseudodip-C14 (testset)other0.03340.9666 other
Pseudodip-C15other0.012820.98718 other
Pseudodip-C16-N (testset)other0.036660.96334 other
Pseudodip-C17other0.004330.99567 other
Pseudodip-C18other0.015240.98476 other
Pseudodip-C19other0.006870.99313 other
Pseudodip-C1other0.007070.99293 other
Pseudodip-C2-Nother0.018570.98143 other
Pseudodip-C3other0.008340.99166 other
Pseudodip-C4other0.152540.84746 other
Pseudodip-C5 (testset)other0.00470.9953 other
Pseudodip-C6other0.01120.9888 other
Pseudodip-C7other0.003310.99669 other
Pseudodip-C8other0.017240.98276 other
Pseudodip-C9other0.005410.99459 other
Pseudodip-R1-N (testset)other0.019240.98076 other
T-ALL-10 (testset)T-ALL0.984250.01575 T-ALL
T-ALL-1 (testset)T-ALL0.940510.05949 T-ALL
T-ALL-2 (testset)T-ALL0.238640.76136 other
T-ALL-3T-ALL0.997020.00298 T-ALL
T-ALL-4 (testset)T-ALL0.990170.00983 T-ALL
T-ALL-5 (testset)T-ALL0.99530.0047 T-ALL
T-ALL-6T-ALL0.989590.01041 T-ALL
T-ALL-7 (testset)T-ALL0.984970.01503 T-ALL
T-ALL-8 (testset)T-ALL0.988290.01171 T-ALL
T-ALL-9T-ALL0.954520.04548 T-ALL
T-ALL-2M1T-ALL0.991620.00838 T-ALL
T-ALL-C10T-ALL0.998040.00196 T-ALL
T-ALL-C11T-ALL0.990280.00972 T-ALL
T-ALL-C12T-ALL0.995520.00448 T-ALL
T-ALL-C13T-ALL0.994580.00542 T-ALL
T-ALL-C14T-ALL0.718820.28118 T-ALL
T-ALL-C15 (testset)T-ALL0.99750.0025 T-ALL
T-ALL-C16 (testset)T-ALL0.698690.30131 T-ALL
T-ALL-C17T-ALL0.755910.24409 T-ALL
T-ALL-C18T-ALL0.88030.1197 T-ALL
T-ALL-C19T-ALL0.979590.02041 T-ALL
T-ALL-C1T-ALL0.870570.12943 T-ALL
T-ALL-C20T-ALL0.9950.005 T-ALL
T-ALL-C21T-ALL0.977940.02206 T-ALL
T-ALL-C22 (testset)T-ALL0.990430.00957 T-ALL
T-ALL-C23T-ALL0.819490.18051 T-ALL
T-ALL-C24 (testset)T-ALL0.971920.02808 T-ALL
T-ALL-C25 (testset)T-ALL0.985590.01441 T-ALL
T-ALL-C26T-ALL0.898110.10189 T-ALL
T-ALL-C2T-ALL0.977030.02297 T-ALL
T-ALL-C3T-ALL0.997660.00234 T-ALL
T-ALL-C4T-ALL0.945070.05493 T-ALL
T-ALL-C5 (testset)T-ALL0.518620.48138 T-ALL
T-ALL-C6T-ALL0.976010.02399 T-ALL
T-ALL-C7 (testset)T-ALL0.974580.02542 T-ALL
T-ALL-C8T-ALL0.721860.27814 T-ALL
T-ALL-C9T-ALL0.982050.01795 T-ALL
T-ALL-R1T-ALL0.971930.02807 T-ALL
T-ALL-R2T-ALL0.98770.0123 T-ALL
T-ALL-R3T-ALL0.983860.01614 T-ALL
T-ALL-R4T-ALL0.970340.02966 T-ALL
T-ALL-R5T-ALL0.895160.10484 T-ALL
T-ALL-R6T-ALL0.942080.05792 T-ALL
TEL-AML1-10other0.012050.98795 other
TEL-AML1-11 (testset)other0.005890.99411 other
TEL-AML1-12other0.015750.98425 other
TEL-AML1-13 (testset)other0.006930.99307 other
TEL-AML1-14other0.007450.99255 other
TEL-AML1-1other0.022040.97796 other
TEL-AML1-2other0.013610.98639 other
TEL-AML1-3other0.011720.98828 other
TEL-AML1-4other0.006530.99347 other
TEL-AML1-5 (testset)other0.010120.98988 other
TEL-AML1-6other0.014620.98538 other
TEL-AML1-7other0.009330.99067 other
TEL-AML1-8 (testset)other0.007070.99293 other
TEL-AML1-9other0.009090.99091 other
TEL-AML1-2M1 (testset)other0.032070.96793 other
TEL-AML1-2M2other0.019820.98018 other
TEL-AML1-2M3other0.011290.98871 other
TEL-AML1-2M4 (testset)other0.015840.98416 other
TEL-AML1-2M5other0.014760.98524 other
TEL-AML1-C10other0.008540.99146 other
TEL-AML1-C11other0.00960.9904 other
TEL-AML1-C12other0.008610.99139 other
TEL-AML1-C13other0.005120.99488 other
TEL-AML1-C14 (testset)other0.007440.99256 other
TEL-AML1-C15other0.01360.9864 other
TEL-AML1-C16other0.006210.99379 other
TEL-AML1-C17other0.019450.98055 other
TEL-AML1-C18other0.007130.99287 other
TEL-AML1-C19 (testset)other0.004430.99557 other
TEL-AML1-C1 (testset)other0.006510.99349 other
TEL-AML1-C20 (testset)other0.004450.99555 other
TEL-AML1-C21other0.014350.98565 other
TEL-AML1-C22other0.014650.98535 other
TEL-AML1-C23 (testset)other0.045310.95469 other
TEL-AML1-C24other0.011570.98843 other
TEL-AML1-C25other0.009620.99038 other
TEL-AML1-C26 (testset)other0.008610.99139 other
TEL-AML1-C27other0.013290.98671 other
TEL-AML1-C28 (testset)other0.009080.99092 other
TEL-AML1-C29other0.010460.98954 other
TEL-AML1-C2other0.009110.99089 other
TEL-AML1-C30other0.013140.98686 other
TEL-AML1-C31 (testset)other0.005120.99488 other
TEL-AML1-C32other0.01060.9894 other
TEL-AML1-C33 (testset)other0.004640.99536 other
TEL-AML1-C34other0.008380.99162 other
TEL-AML1-C35other0.011420.98858 other
TEL-AML1-C36 (testset)other0.009660.99034 other
TEL-AML1-C37other0.023370.97663 other
TEL-AML1-C38other0.007680.99232 other
TEL-AML1-C39other0.008940.99106 other
TEL-AML1-C3other0.006090.99391 other
TEL-AML1-C40other0.009990.99001 other
TEL-AML1-C41other0.016830.98317 other
TEL-AML1-C42other0.030570.96943 other
TEL-AML1-C43other0.012530.98747 other
TEL-AML1-C44other0.005030.99497 other
TEL-AML1-C45other0.014680.98532 other
TEL-AML1-C46other0.009020.99098 other
TEL-AML1-C47other0.004150.99585 other
TEL-AML1-C48other0.089440.91056 other
TEL-AML1-C49 (testset)other0.006730.99327 other
TEL-AML1-C4 (testset)other0.010940.98906 other
TEL-AML1-C50other0.012430.98757 other
TEL-AML1-C51 (testset)other0.02920.9708 other
TEL-AML1-C52other0.017550.98245 other
TEL-AML1-C53 (testset)other0.086780.91322 other
TEL-AML1-C54other0.007330.99267 other
TEL-AML1-C55 (testset)other0.017160.98284 other
TEL-AML1-C56other0.014870.98513 other
TEL-AML1-C57other0.006850.99315 other
TEL-AML1-C5 (testset)other0.009650.99035 other
TEL-AML1-C6other0.003910.99609 other
TEL-AML1-C7other0.010530.98947 other
TEL-AML1-C8other0.045340.95466 other
TEL-AML1-C9other0.022920.97708 other
TEL-AML1-R1 (testset)other0.011760.98824 other
TEL-AML1-R2 (testset)other0.011860.98814 other
TEL-AML1-R3other0.009320.99068 other

 


Generated by StAM on Tue Sep 7 18:29:28 2004