StAM Report: Prediction of ADENO (predictive) - beta 0.886, 0.114

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

Information on Evaluation

Total number of samples:	156
Training samples:	105 ( 93 from ADENO, 12 from NORMAL )
Test samples:	51 ( 46 from ADENO, 5 from NORMAL )
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:	105
Number of classes:	2
Class weights:	'ADENO': 0.886 'NORMAL': 0.114
Class prior:	'ADENO':0.886 'NORMAL':0.114
Shrinkage candidates:	0, 0.024, 0.047, 0.071, 0.095, 0.118, 0.142, 0.166, 0.189, 0.213, 0.237, 0.26, 0.284, 0.308, 0.331, 0.355, 0.378, 0.402, 0.426, 0.449, 0.473, 0.497, 0.52, 0.544, 0.568, 0.591, 0.615, 0.639, 0.662, 0.686

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0	0.24993	2.35139	650	8120
0.024	0	0.24838	2.35299	650	8120
0.047	0	0.24661	2.35489	650	8120
0.071	0	0.24458	2.3572	650	8120
0.095	0	0.24223	2.36006	650	8120
0.118	0	0.23946	2.36505	649	8120
0.142	0	0.23622	2.36774	646	8114
0.166	0	0.23235	2.40696	624	8112
0.189	0	0.2277	2.41246	620	8105
0.213	0	0.2223	2.43949	603	8094
0.237	0	0.21635	2.4682	568	8046
0.26	0	0.20863	2.53488	531	8028
0.284	0	0.19715	2.55294	522	8000
0.308	0	0.18289	2.59211	490	7923
0.331	0	0.17174	2.68369	443	7889
0.355	0	0.16174	2.76248	398	7577
0.378	0	0.15251	2.80116	368	7344
0.402	0	0.14151	2.90809	328	7210
0.426	0	0.12635	2.94631	304	7131
0.449	0	0.10657	3.08216	265	6624
0.473	0	0.08655	3.27815	217	5753
0.497	0	0.07456	3.47718	179	5103
0.52	0	0.06721	3.65288	145	4871
0.544	0	0.06239	4.21011	110	3068
0.568	0	0.0562	4.73749	87	2339
0.591	0	0.05256	5.00049	74	1960
0.615	0	0.04819	6.24604	54	1403
0.639	0	0.0507	6.52183	44	862
0.662	0	0.05603	7.60001	16	321

Information on Model Fit

Fit for D = 0.5677

Number of classes:	2
Class weights:	'ADENO': 0.886 'NORMAL': 0.114
Class prior:	'ADENO':0.886 'NORMAL':0.114
Chosen shrinkage level:	0.568 (by optimizing the root's error rate )
Number of nodes left	87
Number of accessible genes	2339

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:	156 (139 from ADENO, 17 from NORMAL)
Test samples:	51 (46 from ADENO, 5 from NORMAL)
Classes:	ADENO, NORMAL

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	0.25546
GO:0007275	development	0.24926
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.22272
GO:0050789	regulation of biological process	0.27256
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0
• Performance: 0.05621
• Redundancy: 4.35525

	Sensitivity	Specificity
ADENO	1	1
NORMAL	1	1

Performance on test data

• Error rate: 0.05882
• Performance: 0.26793
• Redundancy: 4.53887

	Sensitivity	Specificity
ADENO	0.93478	1
NORMAL	1	0.93478

Predictions

	Class	ADENO	NORMAL	Predictionn
CL2001031608AA	ADENO	0.95872	0.04128	ADENO
CL2001031611AA (testset)	ADENO	0.99699	0.00301	ADENO
CL2001031612AA	ADENO	0.95362	0.04638	ADENO
CL2001031613AA	ADENO	0.87566	0.12434	ADENO
CL2001031615AA	ADENO	0.99848	0.00152	ADENO
CL2001031616AA	ADENO	0.99637	0.00363	ADENO
CL2001031618AA (testset)	ADENO	0.99373	0.00627	ADENO
CL2001031622AA	ADENO	0.99909	0.00091	ADENO
CL2001031625AA (testset)	ADENO	0.9959	0.0041	ADENO
CL2001031627AA	ADENO	0.99281	0.00719	ADENO
CL2001031628AA	ADENO	0.99401	0.00599	ADENO
CL2001031629AA	ADENO	0.99921	0.00079	ADENO
CL2001031630AA	ADENO	0.99816	0.00184	ADENO
CL2001031631AA	ADENO	0.99825	0.00175	ADENO
CL2001031632AA	ADENO	0.99899	0.00101	ADENO
CL2001031634AA	ADENO	0.98426	0.01574	ADENO
CL2001031635AA	ADENO	0.99485	0.00515	ADENO
CL2001031636AA	ADENO	0.99785	0.00215	ADENO
CL2001032002AA	ADENO	0.99708	0.00292	ADENO
CL2001032005AA	ADENO	0.99874	0.00126	ADENO
CL2001032008AA	ADENO	0.99919	0.00081	ADENO
CL2001032009AA (testset)	ADENO	0.99897	0.00103	ADENO
CL2001032011AA	ADENO	0.9573	0.0427	ADENO
CL2001032012AA (testset)	ADENO	0.97904	0.02096	ADENO
CL2001032013AA (testset)	ADENO	0.98754	0.01246	ADENO
CL2001032015AA	ADENO	0.87019	0.12981	ADENO
CL2001032016AA	ADENO	0.99852	0.00148	ADENO
CL2001032019AA	ADENO	0.99524	0.00476	ADENO
CL2001032020AA	ADENO	0.99166	0.00834	ADENO
CL2001032025AA	ADENO	0.99547	0.00453	ADENO
CL2001032026AA	ADENO	0.9987	0.0013	ADENO
CL2001032027AA (testset)	ADENO	0.99155	0.00845	ADENO
CL2001032030AA (testset)	ADENO	0.9983	0.0017	ADENO
CL2001032031AA	ADENO	0.97737	0.02263	ADENO
CL2001032032AA (testset)	ADENO	0.98494	0.01506	ADENO
CL2001032034AA (testset)	ADENO	0.46273	0.53727	NORMAL
CL2001032036AA	ADENO	0.99045	0.00955	ADENO
CL2001032103AA	ADENO	0.99751	0.00249	ADENO
CL2001032104AA (testset)	ADENO	0.99711	0.00289	ADENO
CL2001032105AA	ADENO	0.99862	0.00138	ADENO
CL2001032107AA	ADENO	0.99871	0.00129	ADENO
CL2001032108AA (testset)	ADENO	0.98942	0.01058	ADENO
CL2001032109AA	ADENO	0.96364	0.03636	ADENO
CL2001032110AA	ADENO	0.98573	0.01427	ADENO
CL2001032111AA	ADENO	0.98388	0.01612	ADENO
CL2001032113AA	ADENO	0.99907	0.00093	ADENO
CL2001032114AA	ADENO	0.99723	0.00277	ADENO
CL2001032115AA (testset)	ADENO	0.99888	0.00112	ADENO
CL2001032116AA (testset)	ADENO	0.99698	0.00302	ADENO
CL2001032117AA	ADENO	0.9934	0.0066	ADENO
CL2001032125AA (testset)	ADENO	0.99912	0.00088	ADENO
CL2001032130AA	ADENO	0.99812	0.00188	ADENO
CL2001032132AA	ADENO	0.99616	0.00384	ADENO
CL2001032134AA (testset)	ADENO	0.96463	0.03537	ADENO
CL2001032135AA	ADENO	0.98548	0.01452	ADENO
CL2001032136AA	ADENO	0.99347	0.00653	ADENO
CL2001032138AA	ADENO	0.99387	0.00613	ADENO
CL2001032141AA	ADENO	0.99658	0.00342	ADENO
CL2001032142AA	ADENO	0.99553	0.00447	ADENO
CL2001032149AA (testset)	ADENO	0.95459	0.04541	ADENO
CL2001032155AA (testset)	ADENO	0.24356	0.75644	NORMAL
CL2001032156AA	ADENO	0.98294	0.01706	ADENO
CL2001032211AA (testset)	ADENO	0.99939	0.00061	ADENO
CL2001032212AA	ADENO	0.99887	0.00113	ADENO
CL2001032213AA	ADENO	0.97159	0.02841	ADENO
CL2001032214AA	ADENO	0.90857	0.09143	ADENO
CL2001032229AA	ADENO	0.99706	0.00294	ADENO
CL2001032232AA (testset)	ADENO	0.99754	0.00246	ADENO
CL2001032233AA	ADENO	0.99825	0.00175	ADENO
CL2001032241AA	ADENO	0.99088	0.00912	ADENO
CL2001032242AA	ADENO	0.99887	0.00113	ADENO
CL2001032243AA	ADENO	0.98928	0.01072	ADENO
CL2001032248AA	ADENO	0.99953	0.00047	ADENO
CL2001032249AA (testset)	ADENO	0.99147	0.00853	ADENO
CL2001032252AA	ADENO	0.99378	0.00622	ADENO
CL2001032254AA	ADENO	0.99724	0.00276	ADENO
CL2001032255AA	ADENO	0.99581	0.00419	ADENO
CL2001032259AA	ADENO	0.9978	0.0022	ADENO
CL2001032301AA (testset)	ADENO	0.99381	0.00619	ADENO
CL2001032306AA	ADENO	0.98849	0.01151	ADENO
CL2001032307AA	ADENO	0.75269	0.24731	ADENO
CL2001032308AA (testset)	ADENO	0.9963	0.0037	ADENO
CL2001032309AA	ADENO	0.99852	0.00148	ADENO
CL2001032310AA (testset)	ADENO	0.9976	0.0024	ADENO
CL2001032311AA	ADENO	0.99879	0.00121	ADENO
CL2001032312AA	ADENO	0.99509	0.00491	ADENO
CL2001032313AA (testset)	ADENO	0.99797	0.00203	ADENO
CL2001032314AA (testset)	ADENO	0.98445	0.01555	ADENO
CL2001032316AA	ADENO	0.99693	0.00307	ADENO
CL2001032601AA (testset)	ADENO	0.9991	9e-04	ADENO
CL2001032602AA (testset)	ADENO	0.99814	0.00186	ADENO
CL2001032604AA	ADENO	0.99789	0.00211	ADENO
CL2001032610AA	ADENO	0.99805	0.00195	ADENO
CL2001032612AA	ADENO	0.99381	0.00619	ADENO
CL2001032613AA	ADENO	0.99781	0.00219	ADENO
CL2001032614AA	ADENO	0.99932	0.00068	ADENO
CL2001032616AA (testset)	ADENO	0.99392	0.00608	ADENO
CL2001032617AA (testset)	ADENO	0.99927	0.00073	ADENO
CL2001032620AA	ADENO	0.99845	0.00155	ADENO
CL2001032625AA	ADENO	0.99925	0.00075	ADENO
CL2001032628AA	ADENO	0.99772	0.00228	ADENO
CL2001032638AA (testset)	ADENO	0.99695	0.00305	ADENO
CL2001032640AA	ADENO	0.99718	0.00282	ADENO
CL2001032643AA (testset)	ADENO	0.99734	0.00266	ADENO
CL2001032647AA	ADENO	0.97768	0.02232	ADENO
CL2001032701AA (testset)	ADENO	0.99842	0.00158	ADENO
CL2001032702AA	ADENO	0.99568	0.00432	ADENO
CL2001032703AA (testset)	ADENO	0.9983	0.0017	ADENO
CL2001032704AA (testset)	ADENO	0.99497	0.00503	ADENO
CL2001032706AA	ADENO	0.994	0.006	ADENO
CL2001032709AA	ADENO	0.99832	0.00168	ADENO
CL2001032716AA	ADENO	0.98593	0.01407	ADENO
CL2001032717AA	ADENO	0.99784	0.00216	ADENO
CL2001032729AA	ADENO	0.99808	0.00192	ADENO
CL2001032730AA	ADENO	0.99861	0.00139	ADENO
CL2001032733AA (testset)	ADENO	0.99837	0.00163	ADENO
CL2001032738AA (testset)	ADENO	0.9987	0.0013	ADENO
CL2001032742AA	ADENO	0.9832	0.0168	ADENO
CL2001032746AA	ADENO	0.99639	0.00361	ADENO
CL2001032747AA	ADENO	0.99742	0.00258	ADENO
CL2001032833AA (testset)	ADENO	0.99803	0.00197	ADENO
CL2001032836AA	ADENO	0.99892	0.00108	ADENO
CL2001032838AA	ADENO	0.99727	0.00273	ADENO
CL2001032839AA	ADENO	0.99002	0.00998	ADENO
CL2001032841AA (testset)	ADENO	0.99825	0.00175	ADENO
CL2001032842AA	ADENO	0.99901	0.00099	ADENO
CL2001032843AA (testset)	ADENO	0.99832	0.00168	ADENO
CL2001032845AA (testset)	ADENO	0.99671	0.00329	ADENO
CL2001032846AA	ADENO	0.99569	0.00431	ADENO
CL2001032848AA (testset)	ADENO	0.01386	0.98614	NORMAL
CL2001032856AA	ADENO	0.99821	0.00179	ADENO
CL2001032857AA	ADENO	0.99671	0.00329	ADENO
CL2001040305AA (testset)	ADENO	0.99865	0.00135	ADENO
CL2001040306AA (testset)	ADENO	0.99521	0.00479	ADENO
CL2001041708AA (testset)	ADENO	0.99744	0.00256	ADENO
CL2001041711AA	ADENO	0.99662	0.00338	ADENO
CL2001041716AA	ADENO	0.95321	0.04679	ADENO
CL2001042505AA (testset)	ADENO	0.99869	0.00131	ADENO
CL2001042506AA	ADENO	0.91689	0.08311	ADENO
CL2001032010AA (testset)	NORMAL	0.10301	0.89699	NORMAL
CL2001032041AA	NORMAL	0.05382	0.94618	NORMAL
CL2001032043AA (testset)	NORMAL	0.00506	0.99494	NORMAL
CL2001032045AA	NORMAL	0.03681	0.96319	NORMAL
CL2001032046AA	NORMAL	0.03076	0.96924	NORMAL
CL2001032102AA	NORMAL	0.00413	0.99587	NORMAL
CL2001032128AA (testset)	NORMAL	0.03124	0.96876	NORMAL
CL2001032147AA	NORMAL	0.00622	0.99378	NORMAL
CL2001032202AA	NORMAL	0.003	0.997	NORMAL
CL2001032206AA (testset)	NORMAL	0.03622	0.96378	NORMAL
CL2001032220AA	NORMAL	0.00947	0.99053	NORMAL
CL2001032256AA	NORMAL	0.33239	0.66761	NORMAL
CL2001032304AA	NORMAL	0.08873	0.91127	NORMAL
CL2001032718AA	NORMAL	0.00586	0.99414	NORMAL
CL2001032724AA	NORMAL	0.23193	0.76807	NORMAL
CL2001032725AA (testset)	NORMAL	0.01451	0.98549	NORMAL
CL2001032727AA	NORMAL	0.0084	0.9916	NORMAL