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

• 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:	38 ( 17 from NORMAL, 21 from SQUAMOUS )
Test samples:	38 ( 17 from NORMAL, 21 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:	38
Number of classes:	2
Class weights:	'NORMAL': 0.1 'SQUAMOUS': 0.9
Class prior:	'NORMAL':0.447 'SQUAMOUS':0.553
Shrinkage candidates:	0, 0.042, 0.085, 0.127, 0.169, 0.212, 0.254, 0.297, 0.339, 0.381, 0.424, 0.466, 0.508, 0.551, 0.593, 0.635, 0.678, 0.72, 0.762, 0.805, 0.847, 0.89, 0.932, 0.974, 1.017, 1.059, 1.101, 1.144, 1.186, 1.228

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0	0.44024	0.80529	1928	8646
0.042	0	0.40612	0.81647	1861	8640
0.085	0	0.36971	0.84011	1709	8622
0.127	0	0.34592	0.86368	1586	8601
0.169	0	0.33199	0.88925	1471	8574
0.212	0	0.31767	0.91959	1354	8541
0.254	0	0.30278	0.9639	1209	8496
0.297	0	0.28812	1.02064	1073	8398
0.339	0	0.27325	1.09191	939	8120
0.381	0	0.25888	1.15642	854	7869
0.424	0	0.2489	1.21024	793	7682
0.466	0	0.23756	1.28602	722	7456
0.508	0	0.22438	1.37732	654	7347
0.551	0	0.20994	1.4845	585	6726
0.593	0	0.19826	1.60607	519	6321
0.635	0	0.18473	1.72073	476	5742
0.678	0	0.17136	1.85287	434	5521
0.72	0	0.16009	1.94324	403	5227
0.762	0	0.14733	2.24026	337	4998
0.805	0	0.13284	2.39122	308	4666
0.847	0	0.115	2.58674	282	4545
0.89	0	0.09826	2.94556	237	4348
0.932	0	0.08439	3.15143	219	4227
0.974	0	0.06863	3.54057	186	3967
1.017	0	0.05399	3.42211	175	3860
1.059	0	0.04334	4.01253	142	3356
1.101	0	0.03472	4.5676	112	3015
1.144	0	0.02825	5.36326	82	2405
1.186	0	0.02191	6.96093	55	1760

Information on Model Fit

Performance vs. redundancy

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	Best Delta	Root Error Rate	Performance	Redundancy	#Nodes	#Genes
0	0	0	0.4402	0.8053	1928	8646
0.1	0.1271	0	0.3459	0.8637	1586	8601
0.2	0.2541	0	0.3028	0.9639	1209	8496
0.3	0.4236	0	0.2489	1.2102	793	7682
0.4	0.7201	0	0.1601	1.9432	403	5227
0.5	1.0166	0	0.054	3.4221	175	3860
0.6	1.0166	0	0.054	3.4221	175	3860
0.7	1.0166	0	0.054	3.4221	175	3860
0.8	1.0589	0	0.0433	4.0125	142	3356
0.9	1.1437	0	0.0283	5.3633	82	2405
1	1.186	0	0.0219	6.9609	55	1760

Fit for D = 1.1437

Number of classes:	2
Class weights:	'NORMAL': 0.1 'SQUAMOUS': 0.9
Class prior:	'NORMAL':0.447 'SQUAMOUS':0.553
Chosen shrinkage level:	1.144 (by accepting the system default (after consulting weighting alternatives) )
Number of nodes left	82
Number of accessible genes	2405

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:	38 (17 from NORMAL, 21 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	0.29197
GO:0009987	cellular process	0.24283
GO:0007275	development	0.23437
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.23083
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0
• Performance: 0.02825
• Redundancy: 4.73547

	Sensitivity	Specificity
NORMAL	1	1
SQUAMOUS	1	1

Performance on test data

• Error rate: 0
• Performance: 0.01426
• Redundancy: 5.09387

	Sensitivity	Specificity
NORMAL	1	1
SQUAMOUS	1	1

Predictions

	Class	NORMAL	SQUAMOUS	Predictionn
CL2001031606AA (testset)	SQUAMOUS	0.01993	0.98007	SQUAMOUS
CL2001031620AA (testset)	SQUAMOUS	0.00051	0.99949	SQUAMOUS
CL2001031621AA (testset)	SQUAMOUS	0.00184	0.99816	SQUAMOUS
CL2001032122AA (testset)	SQUAMOUS	0.00151	0.99849	SQUAMOUS
CL2001032129AA (testset)	SQUAMOUS	0.00193	0.99807	SQUAMOUS
CL2001032144AA (testset)	SQUAMOUS	0.00124	0.99876	SQUAMOUS
CL2001032153AA (testset)	SQUAMOUS	0.00802	0.99198	SQUAMOUS
CL2001032207AA (testset)	SQUAMOUS	0.00136	0.99864	SQUAMOUS
CL2001032209AA (testset)	SQUAMOUS	0.00204	0.99796	SQUAMOUS
CL2001032218AA (testset)	SQUAMOUS	0.00357	0.99643	SQUAMOUS
CL2001032222AA (testset)	SQUAMOUS	0.00113	0.99887	SQUAMOUS
CL2001032231AA (testset)	SQUAMOUS	0.02658	0.97342	SQUAMOUS
CL2001032239AA (testset)	SQUAMOUS	0.02955	0.97045	SQUAMOUS
CL2001032240AA (testset)	SQUAMOUS	0.00318	0.99682	SQUAMOUS
CL2001032305AA (testset)	SQUAMOUS	0.01682	0.98318	SQUAMOUS
CL2001032608AA (testset)	SQUAMOUS	0.00192	0.99808	SQUAMOUS
CL2001032627AA (testset)	SQUAMOUS	2e-04	0.9998	SQUAMOUS
CL2001032644AA (testset)	SQUAMOUS	0.00101	0.99899	SQUAMOUS
CL2001032719AA (testset)	SQUAMOUS	0.00681	0.99319	SQUAMOUS
CL2001032732AA (testset)	SQUAMOUS	0.00576	0.99424	SQUAMOUS
CL2001032853AA (testset)	SQUAMOUS	0.00239	0.99761	SQUAMOUS
CL2001032010AA (testset)	NORMAL	0.99665	0.00335	NORMAL
CL2001032041AA (testset)	NORMAL	0.99506	0.00494	NORMAL
CL2001032043AA (testset)	NORMAL	0.999	0.001	NORMAL
CL2001032045AA (testset)	NORMAL	0.9931	0.0069	NORMAL
CL2001032046AA (testset)	NORMAL	0.99814	0.00186	NORMAL
CL2001032102AA (testset)	NORMAL	0.99975	0.00025	NORMAL
CL2001032128AA (testset)	NORMAL	0.99943	0.00057	NORMAL
CL2001032147AA (testset)	NORMAL	0.99967	0.00033	NORMAL
CL2001032202AA (testset)	NORMAL	0.99967	0.00033	NORMAL
CL2001032206AA (testset)	NORMAL	0.98719	0.01281	NORMAL
CL2001032220AA (testset)	NORMAL	0.99913	0.00087	NORMAL
CL2001032256AA (testset)	NORMAL	0.96503	0.03497	NORMAL
CL2001032304AA (testset)	NORMAL	0.95585	0.04415	NORMAL
CL2001032718AA (testset)	NORMAL	0.99929	0.00071	NORMAL
CL2001032724AA (testset)	NORMAL	0.95038	0.04962	NORMAL
CL2001032725AA (testset)	NORMAL	0.9649	0.0351	NORMAL
CL2001032727AA (testset)	NORMAL	0.99884	0.00116	NORMAL