StAM Report: Prediction of SQUAMOUS (predictive) - beta 0.44, 0.56

• Evaluation information
• Annotation information
• Cross validation information
• Model fit information
• Prediction information
• Details on nodes

Information on Evaluation

Total number of samples:	38
Training samples:	25 ( 11 from NORMAL, 14 from SQUAMOUS )
Test samples:	13 ( 6 from NORMAL, 7 from SQUAMOUS )
Focus on class:	SQUAMOUS
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:	25
Number of classes:	2
Class weights:	'NORMAL': 0.44 'SQUAMOUS': 0.56
Class prior:	'NORMAL':0.44 'SQUAMOUS':0.56
Shrinkage candidates:	0, 0.047, 0.095, 0.142, 0.189, 0.237, 0.284, 0.331, 0.378, 0.426, 0.473, 0.52, 0.568, 0.615, 0.662, 0.71, 0.757, 0.804, 0.851, 0.899, 0.946, 0.993, 1.041, 1.088, 1.135, 1.183, 1.23, 1.277, 1.324, 1.372

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0	0.73652	0.79999	1890	8641
0.047	0	0.69989	0.80967	1827	8631
0.095	0	0.65782	0.82397	1731	8614
0.142	0	0.61903	0.84314	1613	8597
0.189	0	0.58384	0.86596	1490	8581
0.237	0	0.55762	0.89361	1363	8542
0.284	0	0.5321	0.93135	1225	8490
0.331	0	0.50499	0.96836	1120	8399
0.378	0	0.4739	1.03539	964	8284
0.426	0	0.44404	1.07427	896	8112
0.473	0	0.41137	1.1393	804	7688
0.52	0	0.38214	1.2034	725	7311
0.568	0	0.34882	1.30896	631	6988
0.615	0	0.32896	1.43068	552	6790
0.662	0	0.31028	1.54364	496	5716
0.71	0	0.29077	1.65423	453	5574
0.757	0	0.27454	1.7951	403	5025
0.804	0	0.26126	1.94428	365	4534
0.851	0	0.24338	2.02983	340	4341
0.899	0	0.2173	2.20331	294	4039
0.946	0	0.19606	2.39644	260	3633
0.993	0	0.17476	2.59706	229	3475
1.041	0	0.15026	2.77556	209	3359
1.088	0	0.12327	2.86404	195	3302
1.135	0	0.09242	2.98398	175	3119
1.183	0	0.07554	3.19005	159	2815
1.23	0	0.06492	3.81895	102	2546
1.277	0	0.04753	4.46309	74	1838
1.324	0	0.02936	6.23599	46	1272

Information on Model Fit

Fit for D = 1.2771

Number of classes:	2
Class weights:	'NORMAL': 0.44 'SQUAMOUS': 0.56
Class prior:	'NORMAL':0.44 'SQUAMOUS':0.56
Chosen shrinkage level:	1.277 (by optimizing the root's error rate )
Number of nodes left	74
Number of accessible genes	1838

Shrunken prediction graph

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Nodewise evaluation

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Information on Predictions

Number of samples:	38 (17 from NORMAL, 21 from SQUAMOUS)
Test samples:	13 (6 from NORMAL, 7 from SQUAMOUS)
Classes:	NORMAL, SQUAMOUS

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

GO:0003673	Gene_Ontology (not in fit)

8 child nodes

ID	Term	Weight
GO:0007610	behavior	0.00000
GO:0000004	biological_process unknown	0.00000
GO:0009987	cellular process	0.37543
GO:0007275	development	0.28524
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.33933
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0
• Performance: 0.04754
• Redundancy: 4.07848

	Sensitivity	Specificity
NORMAL	1	1
SQUAMOUS	1	1

Performance on test data

• Error rate: 0
• Performance: 0.07167
• Redundancy: 3.54302

	Sensitivity	Specificity
NORMAL	1	1
SQUAMOUS	1	1

Predictions

	Class	NORMAL	SQUAMOUS	Predictionn
CL2001031606AA	SQUAMOUS	0.00591	0.99409	SQUAMOUS
CL2001031620AA (testset)	SQUAMOUS	0.01133	0.98867	SQUAMOUS
CL2001031621AA	SQUAMOUS	0.00355	0.99645	SQUAMOUS
CL2001032122AA	SQUAMOUS	0.0066	0.9934	SQUAMOUS
CL2001032129AA (testset)	SQUAMOUS	0.00749	0.99251	SQUAMOUS
CL2001032144AA	SQUAMOUS	0.00359	0.99641	SQUAMOUS
CL2001032153AA	SQUAMOUS	0.07787	0.92213	SQUAMOUS
CL2001032207AA (testset)	SQUAMOUS	0.00701	0.99299	SQUAMOUS
CL2001032209AA	SQUAMOUS	0.00083	0.99917	SQUAMOUS
CL2001032218AA (testset)	SQUAMOUS	0.01994	0.98006	SQUAMOUS
CL2001032222AA	SQUAMOUS	0.00264	0.99736	SQUAMOUS
CL2001032231AA (testset)	SQUAMOUS	0.21814	0.78186	SQUAMOUS
CL2001032239AA (testset)	SQUAMOUS	0.02571	0.97429	SQUAMOUS
CL2001032240AA	SQUAMOUS	0.02031	0.97969	SQUAMOUS
CL2001032305AA	SQUAMOUS	0.02304	0.97696	SQUAMOUS
CL2001032608AA	SQUAMOUS	0.00634	0.99366	SQUAMOUS
CL2001032627AA (testset)	SQUAMOUS	0.00394	0.99606	SQUAMOUS
CL2001032644AA	SQUAMOUS	0.0044	0.9956	SQUAMOUS
CL2001032719AA	SQUAMOUS	0.01035	0.98965	SQUAMOUS
CL2001032732AA	SQUAMOUS	0.00648	0.99352	SQUAMOUS
CL2001032853AA	SQUAMOUS	0.01457	0.98543	SQUAMOUS
CL2001032010AA (testset)	NORMAL	0.97265	0.02735	NORMAL
CL2001032041AA	NORMAL	0.99564	0.00436	NORMAL
CL2001032043AA	NORMAL	0.99943	0.00057	NORMAL
CL2001032045AA (testset)	NORMAL	0.97235	0.02765	NORMAL
CL2001032046AA	NORMAL	0.99673	0.00327	NORMAL
CL2001032102AA	NORMAL	0.99901	0.00099	NORMAL
CL2001032128AA (testset)	NORMAL	0.99679	0.00321	NORMAL
CL2001032147AA	NORMAL	0.9991	9e-04	NORMAL
CL2001032202AA (testset)	NORMAL	0.99342	0.00658	NORMAL
CL2001032206AA	NORMAL	0.99288	0.00712	NORMAL
CL2001032220AA	NORMAL	0.99759	0.00241	NORMAL
CL2001032256AA	NORMAL	0.90344	0.09656	NORMAL
CL2001032304AA	NORMAL	0.97507	0.02493	NORMAL
CL2001032718AA	NORMAL	0.99791	0.00209	NORMAL
CL2001032724AA (testset)	NORMAL	0.93688	0.06312	NORMAL
CL2001032725AA	NORMAL	0.99015	0.00985	NORMAL
CL2001032727AA (testset)	NORMAL	0.99358	0.00642	NORMAL