StAM Report: Prediction of ADENO (predictive) - beta 0.684, 0.316



Information on Evaluation

Total number of samples: 203
Training samples: 136 ( 93 from ADENO, 43 from other )
Test samples: 67 ( 46 from ADENO, 21 from other )
Focus on class: ADENO
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: 136
Number of classes: 2
Class weights: 'ADENO': 0.684 'other': 0.316
Class prior: 'ADENO':0.684 'other':0.316
Shrinkage candidates: 0, 0.034, 0.068, 0.102, 0.137, 0.171, 0.205, 0.239, 0.273, 0.307, 0.342, 0.376, 0.41, 0.444, 0.478, 0.512, 0.547, 0.581, 0.615, 0.649, 0.683, 0.717, 0.751, 0.786, 0.82, 0.854, 0.888, 0.922, 0.956, 0.991


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
00.080880.653530.9413712448467
0.0340.080880.634240.9478912228463
0.0680.051470.613180.9637211368340
0.1020.073530.587340.990919948288
0.1370.073530.561421.031978428196
0.1710.073530.535161.076767218138
0.2050.073530.512541.123936288081
0.2390.073530.49421.186115357863
0.2730.073530.475041.251124707756
0.3070.073530.457551.33584017607
0.3420.073530.442671.435473477466
0.3760.066180.429711.483623187274
0.410.102940.415451.581362777164
0.4440.102940.405671.669072447013
0.4780.102940.397581.721662236772
0.5120.102940.388851.968761806596
0.5470.102940.380861.992141746544
0.5810.102940.37392.114341566359
0.6150.080880.367472.214521305854
0.6490.058820.358122.187921165268
0.6830.058820.33652.50304754644
0.7170.066180.30753.47239483951
0.7510.088240.291933.34618443458
0.7860.073530.282213.9376322887
0.820.066180.27054.19286292440
0.8540.058820.268054.37322272329
0.8880.058820.281974.12074222195
0.9220.051470.277115.825936329
0.9560.044120.26745.95376329


Information on Model Fit


Fit for D = 0.9564

Number of classes: 2
Class weights: 'ADENO': 0.684 'other': 0.316
Class prior: 'ADENO':0.684 'other':0.316
Chosen shrinkage level: 0.956
(by optimizing the root's error rate )
Number of nodes left 6
Number of accessible genes 329

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: 203 (139 from ADENO, 64 from other)
Test samples: 67 (46 from ADENO, 21 from other)
Classes: ADENO, 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
ADENO0.956990.93023
other0.930230.95699

Performance on test data

 SensitivitySpecificity
ADENO0.869570.85714
other0.857140.86957

Predictions

 ClassADENOotherPredictionn
CL2001031606AAother0.001220.99878 other
CL2001031607AAother0.00170.9983 other
CL2001031608AAADENO0.979250.02075 ADENO
CL2001031609AA (testset)other01 other
CL2001031611AAADENO0.804340.19566 ADENO
CL2001031612AA (testset)ADENO0.936070.06393 ADENO
CL2001031613AAADENO0.999060.00094 ADENO
CL2001031615AAADENO0.996390.00361 ADENO
CL2001031616AAADENO0.994610.00539 ADENO
CL2001031618AAADENO0.99946e-04 ADENO
CL2001031620AA (testset)other0.127660.87234 other
CL2001031621AAother0.024470.97553 other
CL2001031622AAADENO0.05370.9463 other
CL2001031625AA (testset)ADENO0.999955e-05 ADENO
CL2001031627AAADENO0.996430.00357 ADENO
CL2001031628AAADENO0.999982e-05 ADENO
CL2001031629AAADENO0.980760.01924 ADENO
CL2001031630AA (testset)ADENO0.999973e-05 ADENO
CL2001031631AA (testset)ADENO0.999982e-05 ADENO
CL2001031632AA (testset)ADENO0.866030.13397 ADENO
CL2001031634AA (testset)ADENO0.997410.00259 ADENO
CL2001031635AAADENO0.997660.00234 ADENO
CL2001031636AAADENO0.941810.05819 ADENO
CL2001032002AAADENO0.999740.00026 ADENO
CL2001032005AA (testset)ADENO0.057520.94248 other
CL2001032008AAADENO0.999982e-05 ADENO
CL2001032009AAADENO0.999760.00024 ADENO
CL2001032010AA (testset)other0.879140.12086 ADENO
CL2001032011AAADENO0.977170.02283 ADENO
CL2001032012AA (testset)ADENO0.999660.00034 ADENO
CL2001032013AA (testset)ADENO0.995530.00447 ADENO
CL2001032015AA (testset)ADENO0.978720.02128 ADENO
CL2001032016AAADENO10 ADENO
CL2001032019AAADENO0.999991e-05 ADENO
CL2001032020AAADENO0.99982e-04 ADENO
CL2001032025AAADENO0.997550.00245 ADENO
CL2001032026AAADENO0.980010.01999 ADENO
CL2001032027AAADENO0.997540.00246 ADENO
CL2001032030AAADENO0.990020.00998 ADENO
CL2001032031AAADENO0.997020.00298 ADENO
CL2001032032AA (testset)ADENO0.867550.13245 ADENO
CL2001032034AAADENO0.799060.20094 ADENO
CL2001032036AAADENO0.286610.71339 other
CL2001032041AAother0.035790.96421 other
CL2001032043AAother0.046650.95335 other
CL2001032044AAother01 other
CL2001032045AAother0.088820.91118 other
CL2001032046AA (testset)other0.125120.87488 other
CL2001032101AAother01 other
CL2001032102AA (testset)other0.519280.48072 ADENO
CL2001032103AAADENO0.993180.00682 ADENO
CL2001032104AAADENO0.999982e-05 ADENO
CL2001032105AA (testset)ADENO0.995080.00492 ADENO
CL2001032107AA (testset)ADENO0.9860.014 ADENO
CL2001032108AAADENO0.999820.00018 ADENO
CL2001032109AA (testset)ADENO0.556270.44373 ADENO
CL2001032110AAADENO0.997870.00213 ADENO
CL2001032111AAADENO0.99430.0057 ADENO
CL2001032113AA (testset)ADENO0.963820.03618 ADENO
CL2001032114AAADENO0.999780.00022 ADENO
CL2001032115AAADENO0.999520.00048 ADENO
CL2001032116AA (testset)ADENO0.999946e-05 ADENO
CL2001032117AAADENO10 ADENO
CL2001032121AAother0.000320.99968 other
CL2001032122AA (testset)other0.425880.57412 other
CL2001032124AAother01 other
CL2001032125AAADENO0.972730.02727 ADENO
CL2001032127AA (testset)other01 other
CL2001032128AAother0.024120.97588 other
CL2001032129AAother0.000970.99903 other
CL2001032130AAADENO0.999919e-05 ADENO
CL2001032132AA (testset)ADENO0.996010.00399 ADENO
CL2001032134AA (testset)ADENO0.917860.08214 ADENO
CL2001032135AAADENO0.999880.00012 ADENO
CL2001032136AAADENO0.981280.01872 ADENO
CL2001032138AAADENO0.99973e-04 ADENO
CL2001032141AA (testset)ADENO0.999991e-05 ADENO
CL2001032142AA (testset)ADENO0.262590.73741 other
CL2001032144AAother0.211020.78898 other
CL2001032145AAother01 other
CL2001032147AA (testset)other0.340890.65911 other
CL2001032149AA (testset)ADENO0.930510.06949 ADENO
CL2001032151AAother01 other
CL2001032152AA (testset)other1e-050.99999 other
CL2001032153AA (testset)other0.024580.97542 other
CL2001032155AA (testset)ADENO0.259150.74085 other
CL2001032156AAADENO0.278620.72138 other
CL2001032202AA (testset)other0.117720.88228 other
CL2001032206AAother0.254320.74568 other
CL2001032207AAother0.004480.99552 other
CL2001032209AA (testset)other0.02850.9715 other
CL2001032210AAother01 other
CL2001032211AA (testset)ADENO0.998350.00165 ADENO
CL2001032212AAADENO0.999710.00029 ADENO
CL2001032213AA (testset)ADENO0.101240.89876 other
CL2001032214AAADENO0.975180.02482 ADENO
CL2001032217AA (testset)other0.000560.99944 other
CL2001032218AAother0.020580.97942 other
CL2001032219AAother01 other
CL2001032220AAother0.462260.53774 other
CL2001032222AAother0.393250.60675 other
CL2001032229AA (testset)ADENO0.998990.00101 ADENO
CL2001032231AAother0.25330.7467 other
CL2001032232AAADENO10 ADENO
CL2001032233AAADENO10 ADENO
CL2001032238AAother0.000460.99954 other
CL2001032239AA (testset)other0.004460.99554 other
CL2001032240AA (testset)other0.288480.71152 other
CL2001032241AAADENO0.999530.00047 ADENO
CL2001032242AA (testset)ADENO10 ADENO
CL2001032243AA (testset)ADENO0.999982e-05 ADENO
CL2001032248AAADENO0.999955e-05 ADENO
CL2001032249AAADENO0.999730.00027 ADENO
CL2001032252AAADENO0.99560.0044 ADENO
CL2001032254AAADENO0.999650.00035 ADENO
CL2001032255AA (testset)ADENO0.999540.00046 ADENO
CL2001032256AAother0.934610.06539 ADENO
CL2001032259AAADENO0.999730.00027 ADENO
CL2001032260AAother0.000760.99924 other
CL2001032301AA (testset)ADENO0.263690.73631 other
CL2001032304AA (testset)other0.787160.21284 ADENO
CL2001032305AAother0.673110.32689 ADENO
CL2001032306AA (testset)ADENO0.850370.14963 ADENO
CL2001032307AAADENO0.999430.00057 ADENO
CL2001032308AA (testset)ADENO0.539470.46053 ADENO
CL2001032309AAADENO0.998540.00146 ADENO
CL2001032310AAADENO0.996380.00362 ADENO
CL2001032311AAADENO0.999370.00063 ADENO
CL2001032312AAADENO0.999770.00023 ADENO
CL2001032313AAADENO0.995550.00445 ADENO
CL2001032314AAADENO0.976490.02351 ADENO
CL2001032316AAADENO0.988910.01109 ADENO
CL2001032601AAADENO0.994150.00585 ADENO
CL2001032602AAADENO0.999955e-05 ADENO
CL2001032604AAADENO0.999991e-05 ADENO
CL2001032607AA (testset)other01 other
CL2001032608AAother0.005140.99486 other
CL2001032610AA (testset)ADENO0.966830.03317 ADENO
CL2001032612AAADENO0.893620.10638 ADENO
CL2001032613AAADENO0.999420.00058 ADENO
CL2001032614AA (testset)ADENO0.929160.07084 ADENO
CL2001032616AAADENO0.998740.00126 ADENO
CL2001032617AA (testset)ADENO0.956180.04382 ADENO
CL2001032620AA (testset)ADENO0.999946e-05 ADENO
CL2001032625AAADENO0.556070.44393 ADENO
CL2001032627AA (testset)other0.011580.98842 other
CL2001032628AAADENO0.999390.00061 ADENO
CL2001032629AA (testset)other1e-050.99999 other
CL2001032630AAother1e-040.9999 other
CL2001032632AAother0.001810.99819 other
CL2001032638AAADENO0.993670.00633 ADENO
CL2001032640AAADENO10 ADENO
CL2001032643AAADENO0.999040.00096 ADENO
CL2001032644AAother0.003220.99678 other
CL2001032647AA (testset)ADENO0.999250.00075 ADENO
CL2001032701AAADENO0.999955e-05 ADENO
CL2001032702AAADENO0.999870.00013 ADENO
CL2001032703AA (testset)ADENO0.984650.01535 ADENO
CL2001032704AAADENO0.992380.00762 ADENO
CL2001032706AAADENO0.999790.00021 ADENO
CL2001032709AAADENO0.999937e-05 ADENO
CL2001032716AAADENO0.959970.04003 ADENO
CL2001032717AAADENO0.99760.0024 ADENO
CL2001032718AAother0.023440.97656 other
CL2001032719AAother0.019070.98093 other
CL2001032720AAother0.000860.99914 other
CL2001032722AAother01 other
CL2001032724AAother0.793930.20607 ADENO
CL2001032725AAother0.245110.75489 other
CL2001032727AAother0.039950.96005 other
CL2001032729AAADENO0.995460.00454 ADENO
CL2001032730AAADENO0.99870.0013 ADENO
CL2001032732AAother0.024110.97589 other
CL2001032733AA (testset)ADENO0.999770.00023 ADENO
CL2001032738AAADENO0.995940.00406 ADENO
CL2001032742AA (testset)ADENO0.431320.56868 other
CL2001032746AAADENO0.990050.00995 ADENO
CL2001032747AA (testset)ADENO0.999850.00015 ADENO
CL2001032833AAADENO0.948730.05127 ADENO
CL2001032836AAADENO0.820690.17931 ADENO
CL2001032838AAADENO0.99982e-04 ADENO
CL2001032839AAADENO0.987330.01267 ADENO
CL2001032841AA (testset)ADENO0.999320.00068 ADENO
CL2001032842AA (testset)ADENO0.54170.4583 ADENO
CL2001032843AA (testset)ADENO0.982170.01783 ADENO
CL2001032845AAADENO0.998840.00116 ADENO
CL2001032846AAADENO0.999982e-05 ADENO
CL2001032847AA (testset)other01 other
CL2001032848AAADENO0.140260.85974 other
CL2001032850AAother01 other
CL2001032853AAother0.053510.94649 other
CL2001032854AAother0.000130.99987 other
CL2001032856AAADENO0.9980.002 ADENO
CL2001032857AAADENO0.999340.00066 ADENO
CL2001032860AAother01 other
CL2001040305AAADENO0.997880.00212 ADENO
CL2001040306AA (testset)ADENO0.999730.00027 ADENO
CL2001041708AA (testset)ADENO0.994370.00563 ADENO
CL2001041711AAADENO0.99982e-04 ADENO
CL2001041716AA (testset)ADENO0.994830.00517 ADENO
CL2001042501AA (testset)other01 other
CL2001042505AAADENO0.979010.02099 ADENO
CL2001042506AAADENO0.845820.15418 ADENO

 


Generated by StAM on Tue Sep 7 17:16:35 2004