StAM Report: Prediction of ADENO (explorative) - beta 0.1, 0.9



Information on Evaluation

Total number of samples: 203
Training samples: 203 ( 139 from ADENO, 64 from other )
Test samples: 203 ( 139 from ADENO, 64 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: 203
Number of classes: 2
Class weights: 'ADENO': 0.1 'other': 0.9
Class prior: 'ADENO':0.685 'other':0.315
Shrinkage candidates: 0, 0.095, 0.191, 0.286, 0.382, 0.477, 0.572, 0.668, 0.763, 0.859, 0.954, 1.05, 1.145, 1.24, 1.336, 1.431, 1.527, 1.622, 1.717, 1.813, 1.908, 2.004, 2.099, 2.195, 2.29, 2.385, 2.481, 2.576, 2.672, 2.767


Cross validated performance


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 Root.error.rateRoot.performanceMean.redundancyNodesGenes
00.083741.417480.8640422038678
0.0950.083741.403050.864222038678
0.1910.073891.386710.8641722028574
0.2860.073891.36810.8644122028574
0.3820.073891.346740.8647122028574
0.4770.073891.322070.8650922028574
0.5720.073891.293370.865622028574
0.6680.073891.25980.8663122028574
0.7630.073891.220390.8673722028574
0.8590.068971.174170.8690122018562
0.9540.068971.120730.8728622018562
1.050.068971.066510.9419411968330
1.1450.068971.006520.978029918247
1.240.068970.939021.042647538134
1.3360.068970.872821.107765947991
1.4310.068970.809111.214044467627
1.5270.078820.779521.346623387286
1.6220.088670.760131.490262696830
1.7170.078820.748611.63442206527
1.8130.073890.727921.596092045970
1.9080.078820.686081.718311495511
2.0040.073890.646931.820061124975
2.0990.073890.592922.06824784248
2.1950.078820.5232.47957553662
2.290.083740.477323.3756372797
2.3850.073890.449923.13845292313
2.4810.073890.434284.03873191541
2.5760.078820.427813.37005191541
2.6720.044330.405626.267691136


Information on Model Fit


Performance vs. redundancy


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 Best DeltaRoot Error RatePerformanceRedundancy#Nodes#Genes
000.08371.41750.86422038678
0.10.95410.0691.12070.872922018562
0.21.33580.0690.87281.10785947991
0.31.43120.0690.80911.2144467627
0.41.43120.0690.80911.2144467627
0.52.09910.07390.59292.0682784248
0.62.19450.07880.5232.4796553662
0.72.57620.07880.42783.37191541
0.82.57620.07880.42783.37191541
0.92.57620.07880.42783.37191541
12.67160.04430.40566.267691136


Fit for D = 2.0991

Number of classes: 2
Class weights: 'ADENO': 0.1 'other': 0.9
Class prior: 'ADENO':0.685 'other':0.315
Chosen shrinkage level: 2.099
(by accepting the system default (after consulting weighting alternatives) )
Number of nodes left 78
Number of accessible genes 4248

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)
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
ADENO0.978420.875
other0.8750.97842

Performance on test data

 SensitivitySpecificity
ADENO0.978420.89062
other0.890620.97842

Predictions

 ClassADENOotherPredictionn
CL2001031606AA (testset)other0.332780.66722 other
CL2001031607AA (testset)other0.196320.80368 other
CL2001031608AA (testset)ADENO0.868160.13184 ADENO
CL2001031609AA (testset)other0.018130.98187 other
CL2001031611AA (testset)ADENO0.863340.13666 ADENO
CL2001031612AA (testset)ADENO0.896380.10362 ADENO
CL2001031613AA (testset)ADENO0.939980.06002 ADENO
CL2001031615AA (testset)ADENO0.949370.05063 ADENO
CL2001031616AA (testset)ADENO0.910380.08962 ADENO
CL2001031618AA (testset)ADENO0.945860.05414 ADENO
CL2001031620AA (testset)other0.175340.82466 other
CL2001031621AA (testset)other0.214330.78567 other
CL2001031622AA (testset)ADENO0.438870.56113 other
CL2001031625AA (testset)ADENO0.97540.0246 ADENO
CL2001031627AA (testset)ADENO0.949030.05097 ADENO
CL2001031628AA (testset)ADENO0.983040.01696 ADENO
CL2001031629AA (testset)ADENO0.938350.06165 ADENO
CL2001031630AA (testset)ADENO0.985760.01424 ADENO
CL2001031631AA (testset)ADENO0.988380.01162 ADENO
CL2001031632AA (testset)ADENO0.824540.17546 ADENO
CL2001031634AA (testset)ADENO0.954170.04583 ADENO
CL2001031635AA (testset)ADENO0.943360.05664 ADENO
CL2001031636AA (testset)ADENO0.808270.19173 ADENO
CL2001032002AA (testset)ADENO0.932040.06796 ADENO
CL2001032005AA (testset)ADENO0.678540.32146 ADENO
CL2001032008AA (testset)ADENO0.979140.02086 ADENO
CL2001032009AA (testset)ADENO0.964290.03571 ADENO
CL2001032010AA (testset)other0.776580.22342 ADENO
CL2001032011AA (testset)ADENO0.944450.05555 ADENO
CL2001032012AA (testset)ADENO0.950180.04982 ADENO
CL2001032013AA (testset)ADENO0.945590.05441 ADENO
CL2001032015AA (testset)ADENO0.763380.23662 ADENO
CL2001032016AA (testset)ADENO0.981710.01829 ADENO
CL2001032019AA (testset)ADENO0.990560.00944 ADENO
CL2001032020AA (testset)ADENO0.986030.01397 ADENO
CL2001032025AA (testset)ADENO0.957180.04282 ADENO
CL2001032026AA (testset)ADENO0.888510.11149 ADENO
CL2001032027AA (testset)ADENO0.958890.04111 ADENO
CL2001032030AA (testset)ADENO0.950720.04928 ADENO
CL2001032031AA (testset)ADENO0.924710.07529 ADENO
CL2001032032AA (testset)ADENO0.876560.12344 ADENO
CL2001032034AA (testset)ADENO0.693180.30682 ADENO
CL2001032036AA (testset)ADENO0.393740.60626 other
CL2001032041AA (testset)other0.179340.82066 other
CL2001032043AA (testset)other0.164860.83514 other
CL2001032044AA (testset)other0.032180.96782 other
CL2001032045AA (testset)other0.171950.82805 other
CL2001032046AA (testset)other0.229490.77051 other
CL2001032101AA (testset)other0.088510.91149 other
CL2001032102AA (testset)other0.356750.64325 other
CL2001032103AA (testset)ADENO0.919120.08088 ADENO
CL2001032104AA (testset)ADENO0.962860.03714 ADENO
CL2001032105AA (testset)ADENO0.970440.02956 ADENO
CL2001032107AA (testset)ADENO0.972580.02742 ADENO
CL2001032108AA (testset)ADENO0.966530.03347 ADENO
CL2001032109AA (testset)ADENO0.782430.21757 ADENO
CL2001032110AA (testset)ADENO0.951560.04844 ADENO
CL2001032111AA (testset)ADENO0.949180.05082 ADENO
CL2001032113AA (testset)ADENO0.877630.12237 ADENO
CL2001032114AA (testset)ADENO0.92810.0719 ADENO
CL2001032115AA (testset)ADENO0.916330.08367 ADENO
CL2001032116AA (testset)ADENO0.979550.02045 ADENO
CL2001032117AA (testset)ADENO0.974280.02572 ADENO
CL2001032121AA (testset)other0.072450.92755 other
CL2001032122AA (testset)other0.492580.50742 other
CL2001032124AA (testset)other0.052740.94726 other
CL2001032125AA (testset)ADENO0.757250.24275 ADENO
CL2001032127AA (testset)other0.027140.97286 other
CL2001032128AA (testset)other0.178480.82152 other
CL2001032129AA (testset)other0.116090.88391 other
CL2001032130AA (testset)ADENO0.9750.025 ADENO
CL2001032132AA (testset)ADENO0.951970.04803 ADENO
CL2001032134AA (testset)ADENO0.866210.13379 ADENO
CL2001032135AA (testset)ADENO0.939860.06014 ADENO
CL2001032136AA (testset)ADENO0.942970.05703 ADENO
CL2001032138AA (testset)ADENO0.970930.02907 ADENO
CL2001032141AA (testset)ADENO0.956340.04366 ADENO
CL2001032142AA (testset)ADENO0.513790.48621 ADENO
CL2001032144AA (testset)other0.340050.65995 other
CL2001032145AA (testset)other0.026560.97344 other
CL2001032147AA (testset)other0.258970.74103 other
CL2001032149AA (testset)ADENO0.9290.071 ADENO
CL2001032151AA (testset)other0.016880.98312 other
CL2001032152AA (testset)other0.043060.95694 other
CL2001032153AA (testset)other0.073870.92613 other
CL2001032155AA (testset)ADENO0.743770.25623 ADENO
CL2001032156AA (testset)ADENO0.512180.48782 ADENO
CL2001032202AA (testset)other0.159830.84017 other
CL2001032206AA (testset)other0.333360.66664 other
CL2001032207AA (testset)other0.158370.84163 other
CL2001032209AA (testset)other0.079190.92081 other
CL2001032210AA (testset)other0.046910.95309 other
CL2001032211AA (testset)ADENO0.924940.07506 ADENO
CL2001032212AA (testset)ADENO0.938550.06145 ADENO
CL2001032213AA (testset)ADENO0.60260.3974 ADENO
CL2001032214AA (testset)ADENO0.827210.17279 ADENO
CL2001032217AA (testset)other0.10060.8994 other
CL2001032218AA (testset)other0.243050.75695 other
CL2001032219AA (testset)other0.06390.9361 other
CL2001032220AA (testset)other0.26950.7305 other
CL2001032222AA (testset)other0.54670.4533 ADENO
CL2001032229AA (testset)ADENO0.947270.05273 ADENO
CL2001032231AA (testset)other0.543690.45631 ADENO
CL2001032232AA (testset)ADENO0.988390.01161 ADENO
CL2001032233AA (testset)ADENO0.977440.02256 ADENO
CL2001032238AA (testset)other0.093970.90603 other
CL2001032239AA (testset)other0.136160.86384 other
CL2001032240AA (testset)other0.325840.67416 other
CL2001032241AA (testset)ADENO0.954750.04525 ADENO
CL2001032242AA (testset)ADENO0.979360.02064 ADENO
CL2001032243AA (testset)ADENO0.976170.02383 ADENO
CL2001032248AA (testset)ADENO0.969040.03096 ADENO
CL2001032249AA (testset)ADENO0.964920.03508 ADENO
CL2001032252AA (testset)ADENO0.955080.04492 ADENO
CL2001032254AA (testset)ADENO0.961490.03851 ADENO
CL2001032255AA (testset)ADENO0.964890.03511 ADENO
CL2001032256AA (testset)other0.82470.1753 ADENO
CL2001032259AA (testset)ADENO0.838960.16104 ADENO
CL2001032260AA (testset)other0.10060.8994 other
CL2001032301AA (testset)ADENO0.767210.23279 ADENO
CL2001032304AA (testset)other0.61290.3871 ADENO
CL2001032305AA (testset)other0.609330.39067 ADENO
CL2001032306AA (testset)ADENO0.947720.05228 ADENO
CL2001032307AA (testset)ADENO0.859620.14038 ADENO
CL2001032308AA (testset)ADENO0.778940.22106 ADENO
CL2001032309AA (testset)ADENO0.95150.0485 ADENO
CL2001032310AA (testset)ADENO0.932220.06778 ADENO
CL2001032311AA (testset)ADENO0.943920.05608 ADENO
CL2001032312AA (testset)ADENO0.957680.04232 ADENO
CL2001032313AA (testset)ADENO0.894790.10521 ADENO
CL2001032314AA (testset)ADENO0.896720.10328 ADENO
CL2001032316AA (testset)ADENO0.871040.12896 ADENO
CL2001032601AA (testset)ADENO0.962290.03771 ADENO
CL2001032602AA (testset)ADENO0.977110.02289 ADENO
CL2001032604AA (testset)ADENO0.962910.03709 ADENO
CL2001032607AA (testset)other0.028480.97152 other
CL2001032608AA (testset)other0.162210.83779 other
CL2001032610AA (testset)ADENO0.953370.04663 ADENO
CL2001032612AA (testset)ADENO0.895790.10421 ADENO
CL2001032613AA (testset)ADENO0.964970.03503 ADENO
CL2001032614AA (testset)ADENO0.884510.11549 ADENO
CL2001032616AA (testset)ADENO0.929530.07047 ADENO
CL2001032617AA (testset)ADENO0.918860.08114 ADENO
CL2001032620AA (testset)ADENO0.956540.04346 ADENO
CL2001032625AA (testset)ADENO0.894690.10531 ADENO
CL2001032627AA (testset)other0.232590.76741 other
CL2001032628AA (testset)ADENO0.972860.02714 ADENO
CL2001032629AA (testset)other0.065580.93442 other
CL2001032630AA (testset)other0.128750.87125 other
CL2001032632AA (testset)other0.131970.86803 other
CL2001032638AA (testset)ADENO0.943420.05658 ADENO
CL2001032640AA (testset)ADENO0.976930.02307 ADENO
CL2001032643AA (testset)ADENO0.921020.07898 ADENO
CL2001032644AA (testset)other0.152120.84788 other
CL2001032647AA (testset)ADENO0.951740.04826 ADENO
CL2001032701AA (testset)ADENO0.9680.032 ADENO
CL2001032702AA (testset)ADENO0.979240.02076 ADENO
CL2001032703AA (testset)ADENO0.920760.07924 ADENO
CL2001032704AA (testset)ADENO0.944360.05564 ADENO
CL2001032706AA (testset)ADENO0.970670.02933 ADENO
CL2001032709AA (testset)ADENO0.984720.01528 ADENO
CL2001032716AA (testset)ADENO0.799110.20089 ADENO
CL2001032717AA (testset)ADENO0.926520.07348 ADENO
CL2001032718AA (testset)other0.122240.87776 other
CL2001032719AA (testset)other0.407270.59273 other
CL2001032720AA (testset)other0.063550.93645 other
CL2001032722AA (testset)other0.034570.96543 other
CL2001032724AA (testset)other0.780560.21944 ADENO
CL2001032725AA (testset)other0.26950.7305 other
CL2001032727AA (testset)other0.266960.73304 other
CL2001032729AA (testset)ADENO0.960940.03906 ADENO
CL2001032730AA (testset)ADENO0.964320.03568 ADENO
CL2001032732AA (testset)other0.226730.77327 other
CL2001032733AA (testset)ADENO0.970820.02918 ADENO
CL2001032738AA (testset)ADENO0.889340.11066 ADENO
CL2001032742AA (testset)ADENO0.764810.23519 ADENO
CL2001032746AA (testset)ADENO0.931980.06802 ADENO
CL2001032747AA (testset)ADENO0.926580.07342 ADENO
CL2001032833AA (testset)ADENO0.809450.19055 ADENO
CL2001032836AA (testset)ADENO0.959950.04005 ADENO
CL2001032838AA (testset)ADENO0.98080.0192 ADENO
CL2001032839AA (testset)ADENO0.836820.16318 ADENO
CL2001032841AA (testset)ADENO0.96120.0388 ADENO
CL2001032842AA (testset)ADENO0.917120.08288 ADENO
CL2001032843AA (testset)ADENO0.972320.02768 ADENO
CL2001032845AA (testset)ADENO0.959930.04007 ADENO
CL2001032846AA (testset)ADENO0.982560.01744 ADENO
CL2001032847AA (testset)other0.038850.96115 other
CL2001032848AA (testset)ADENO0.206240.79376 other
CL2001032850AA (testset)other0.035360.96464 other
CL2001032853AA (testset)other0.188420.81158 other
CL2001032854AA (testset)other0.10640.8936 other
CL2001032856AA (testset)ADENO0.957930.04207 ADENO
CL2001032857AA (testset)ADENO0.962070.03793 ADENO
CL2001032860AA (testset)other0.014730.98527 other
CL2001040305AA (testset)ADENO0.949160.05084 ADENO
CL2001040306AA (testset)ADENO0.965020.03498 ADENO
CL2001041708AA (testset)ADENO0.969830.03017 ADENO
CL2001041711AA (testset)ADENO0.946970.05303 ADENO
CL2001041716AA (testset)ADENO0.897220.10278 ADENO
CL2001042501AA (testset)other0.030910.96909 other
CL2001042505AA (testset)ADENO0.878950.12105 ADENO
CL2001042506AA (testset)ADENO0.79880.2012 ADENO

 


Generated by StAM on Tue Sep 7 18:09:03 2004