StAM Report: Prediction of CARCINOID (predictive) - beta 0.103, 0.897

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

Information on Evaluation

Total number of samples:	203
Training samples:	136 ( 14 from CARCINOID, 122 from other )
Test samples:	67 ( 6 from CARCINOID, 61 from other )
Focus on class:	CARCINOID
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:	'CARCINOID': 0.103 'other': 0.897
Class prior:	'CARCINOID':0.103 'other':0.897
Shrinkage candidates:	0, 0.032, 0.064, 0.096, 0.128, 0.161, 0.193, 0.225, 0.257, 0.289, 0.321, 0.353, 0.385, 0.418, 0.45, 0.482, 0.514, 0.546, 0.578, 0.61, 0.642, 0.674, 0.707, 0.739, 0.771, 0.803, 0.835, 0.867, 0.899, 0.931

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.00735	0.33053	1.83049	2203	8575
0.032	0.00735	0.32447	1.83262	2203	8575
0.064	0.00735	0.31754	1.83523	2203	8575
0.096	0.00735	0.3095	1.8385	2203	8575
0.128	0.00735	0.30005	1.84272	2203	8575
0.161	0.00735	0.28868	1.84842	2203	8575
0.193	0.00735	0.27452	1.8566	2203	8575
0.225	0.00735	0.25561	1.86957	2203	8575
0.257	0.00735	0.22625	1.8949	2203	8575
0.289	0	0.20844	2.53804	911	7882
0.321	0	0.20569	2.53893	908	7878
0.353	0	0.20239	2.55093	902	7878
0.385	0	0.19852	2.57078	890	7876
0.418	0	0.19351	2.58752	880	7876
0.45	0	0.18674	2.6036	870	7864
0.482	0	0.17962	2.64001	844	7856
0.514	0	0.17429	2.70369	794	7848
0.546	0	0.16869	2.78299	721	7769
0.578	0	0.1634	2.85542	672	7696
0.61	0	0.15616	2.90365	630	7648
0.642	0	0.14578	2.96427	553	7471
0.674	0	0.13445	3.10826	483	7342
0.707	0	0.11918	3.20541	408	7108
0.739	0	0.1057	3.39494	335	6718
0.771	0	0.08267	3.74979	245	5776
0.803	0	0.05757	4.49638	175	5026
0.835	0	0.04774	5.33156	122	4418
0.867	0	0.03821	6.94347	76	2559
0.899	0	0.02935	11.80487	46	1492

Information on Model Fit

Fit for D = 0.8672

Number of classes:	2
Class weights:	'CARCINOID': 0.103 'other': 0.897
Class prior:	'CARCINOID':0.103 'other':0.897
Chosen shrinkage level:	0.867 (by optimizing the root's error rate )
Number of nodes left	76
Number of accessible genes	2559

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 (20 from CARCINOID, 183 from other)
Test samples:	67 (6 from CARCINOID, 61 from other)
Classes:	CARCINOID, 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

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	0.46772
GO:0007275	development	0.15212
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.38016
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0
• Performance: 0.0382
• Redundancy: 5.14539

	Sensitivity	Specificity
CARCINOID	1	1
other	1	1

Performance on test data

• Error rate: 0
• Performance: 0.0424
• Redundancy: 4.92114

	Sensitivity	Specificity
CARCINOID	1	1
other	1	1

Predictions

	Class	CARCINOID	other	Predictionn
CL2001031606AA (testset)	other	0.00517	0.99483	other
CL2001031607AA	other	0.00929	0.99071	other
CL2001031608AA	other	0.00399	0.99601	other
CL2001031609AA	CARCINOID	0.99257	0.00743	CARCINOID
CL2001031611AA	other	5e-04	0.9995	other
CL2001031612AA (testset)	other	0.00021	0.99979	other
CL2001031613AA	other	0.00054	0.99946	other
CL2001031615AA	other	0.00277	0.99723	other
CL2001031616AA	other	4e-04	0.9996	other
CL2001031618AA	other	0.02495	0.97505	other
CL2001031620AA (testset)	other	0.00274	0.99726	other
CL2001031621AA	other	0.0218	0.9782	other
CL2001031622AA (testset)	other	0.00095	0.99905	other
CL2001031625AA	other	0.01248	0.98752	other
CL2001031627AA	other	0.00142	0.99858	other
CL2001031628AA	other	8e-04	0.9992	other
CL2001031629AA	other	0.00099	0.99901	other
CL2001031630AA	other	0.00307	0.99693	other
CL2001031631AA	other	0.00061	0.99939	other
CL2001031632AA	other	0.00185	0.99815	other
CL2001031634AA	other	0.00308	0.99692	other
CL2001031635AA (testset)	other	0.00376	0.99624	other
CL2001031636AA (testset)	other	0.08914	0.91086	other
CL2001032002AA (testset)	other	0.02312	0.97688	other
CL2001032005AA (testset)	other	0.05229	0.94771	other
CL2001032008AA	other	0.00037	0.99963	other
CL2001032009AA (testset)	other	0.00797	0.99203	other
CL2001032010AA	other	0.00482	0.99518	other
CL2001032011AA	other	0.00386	0.99614	other
CL2001032012AA (testset)	other	0.00173	0.99827	other
CL2001032013AA (testset)	other	0.01122	0.98878	other
CL2001032015AA	other	0.01361	0.98639	other
CL2001032016AA	other	0.00094	0.99906	other
CL2001032019AA	other	0.00124	0.99876	other
CL2001032020AA (testset)	other	0.00041	0.99959	other
CL2001032025AA	other	0.00615	0.99385	other
CL2001032026AA	other	0.00306	0.99694	other
CL2001032027AA (testset)	other	0.00042	0.99958	other
CL2001032030AA	other	0.00031	0.99969	other
CL2001032031AA	other	0.00117	0.99883	other
CL2001032032AA (testset)	other	0.00839	0.99161	other
CL2001032034AA	other	0.0021	0.9979	other
CL2001032036AA	other	0.01704	0.98296	other
CL2001032041AA	other	0.00353	0.99647	other
CL2001032043AA	other	0.01272	0.98728	other
CL2001032044AA (testset)	CARCINOID	0.99787	0.00213	CARCINOID
CL2001032045AA	other	0.01053	0.98947	other
CL2001032046AA	other	0.01681	0.98319	other
CL2001032101AA	CARCINOID	0.99685	0.00315	CARCINOID
CL2001032102AA	other	0.01107	0.98893	other
CL2001032103AA	other	0.02617	0.97383	other
CL2001032104AA	other	0.00067	0.99933	other
CL2001032105AA (testset)	other	0.00447	0.99553	other
CL2001032107AA	other	0.00106	0.99894	other
CL2001032108AA	other	0.01072	0.98928	other
CL2001032109AA (testset)	other	0.05442	0.94558	other
CL2001032110AA (testset)	other	0.00175	0.99825	other
CL2001032111AA	other	0.00236	0.99764	other
CL2001032113AA	other	0.0266	0.9734	other
CL2001032114AA	other	0.00108	0.99892	other
CL2001032115AA	other	0.0636	0.9364	other
CL2001032116AA	other	0.00283	0.99717	other
CL2001032117AA (testset)	other	0.00743	0.99257	other
CL2001032121AA (testset)	other	0.22353	0.77647	other
CL2001032122AA	other	0.001	0.999	other
CL2001032124AA	CARCINOID	0.99748	0.00252	CARCINOID
CL2001032125AA	other	0.01761	0.98239	other
CL2001032127AA (testset)	CARCINOID	0.85798	0.14202	CARCINOID
CL2001032128AA	other	0.00697	0.99303	other
CL2001032129AA	other	0.00042	0.99958	other
CL2001032130AA (testset)	other	0.00038	0.99962	other
CL2001032132AA (testset)	other	0.00202	0.99798	other
CL2001032134AA	other	0.00128	0.99872	other
CL2001032135AA	other	4e-04	0.9996	other
CL2001032136AA	other	0.00041	0.99959	other
CL2001032138AA	other	0.00063	0.99937	other
CL2001032141AA	other	0.00272	0.99728	other
CL2001032142AA (testset)	other	0.02787	0.97213	other
CL2001032144AA	other	0.00015	0.99985	other
CL2001032145AA (testset)	CARCINOID	0.96424	0.03576	CARCINOID
CL2001032147AA	other	0.0053	0.9947	other
CL2001032149AA	other	0.00034	0.99966	other
CL2001032151AA	CARCINOID	0.98927	0.01073	CARCINOID
CL2001032152AA (testset)	CARCINOID	0.98395	0.01605	CARCINOID
CL2001032153AA	other	0.0325	0.9675	other
CL2001032155AA (testset)	other	0.00023	0.99977	other
CL2001032156AA	other	0.00146	0.99854	other
CL2001032202AA (testset)	other	0.01583	0.98417	other
CL2001032206AA	other	0.00453	0.99547	other
CL2001032207AA (testset)	other	0.00204	0.99796	other
CL2001032209AA (testset)	other	0.0686	0.9314	other
CL2001032210AA	CARCINOID	0.98851	0.01149	CARCINOID
CL2001032211AA	other	0.00027	0.99973	other
CL2001032212AA (testset)	other	0.00508	0.99492	other
CL2001032213AA (testset)	other	0.00192	0.99808	other
CL2001032214AA	other	0.00053	0.99947	other
CL2001032217AA (testset)	other	0.14315	0.85685	other
CL2001032218AA (testset)	other	0.0483	0.9517	other
CL2001032219AA (testset)	CARCINOID	0.88163	0.11837	CARCINOID
CL2001032220AA	other	0.02332	0.97668	other
CL2001032222AA (testset)	other	0.0012	0.9988	other
CL2001032229AA (testset)	other	0.00349	0.99651	other
CL2001032231AA	other	0.00134	0.99866	other
CL2001032232AA	other	0.00089	0.99911	other
CL2001032233AA	other	0.00086	0.99914	other
CL2001032238AA	CARCINOID	0.93776	0.06224	CARCINOID
CL2001032239AA	other	0.00299	0.99701	other
CL2001032240AA	other	0.00107	0.99893	other
CL2001032241AA (testset)	other	0.00096	0.99904	other
CL2001032242AA	other	0.00016	0.99984	other
CL2001032243AA (testset)	other	0.00633	0.99367	other
CL2001032248AA	other	0.00044	0.99956	other
CL2001032249AA	other	0.00134	0.99866	other
CL2001032252AA	other	0.00042	0.99958	other
CL2001032254AA (testset)	other	9e-04	0.9991	other
CL2001032255AA	other	0.00072	0.99928	other
CL2001032256AA (testset)	other	0.00113	0.99887	other
CL2001032259AA	other	0.00408	0.99592	other
CL2001032260AA	other	0.1229	0.8771	other
CL2001032301AA	other	6e-04	0.9994	other
CL2001032304AA (testset)	other	0.00185	0.99815	other
CL2001032305AA (testset)	other	0.00138	0.99862	other
CL2001032306AA	other	0.00054	0.99946	other
CL2001032307AA	other	0.00244	0.99756	other
CL2001032308AA	other	0.00853	0.99147	other
CL2001032309AA	other	0.0248	0.9752	other
CL2001032310AA	other	0.0117	0.9883	other
CL2001032311AA	other	0.00106	0.99894	other
CL2001032312AA	other	0.00083	0.99917	other
CL2001032313AA	other	0.00249	0.99751	other
CL2001032314AA	other	0.0018	0.9982	other
CL2001032316AA (testset)	other	0.00974	0.99026	other
CL2001032601AA	other	7e-04	0.9993	other
CL2001032602AA	other	0.00401	0.99599	other
CL2001032604AA	other	0.00131	0.99869	other
CL2001032607AA	CARCINOID	0.98595	0.01405	CARCINOID
CL2001032608AA	other	0.00871	0.99129	other
CL2001032610AA (testset)	other	0.00072	0.99928	other
CL2001032612AA	other	0.00567	0.99433	other
CL2001032613AA (testset)	other	8e-04	0.9992	other
CL2001032614AA (testset)	other	0.00178	0.99822	other
CL2001032616AA	other	0.01252	0.98748	other
CL2001032617AA (testset)	other	0.00112	0.99888	other
CL2001032620AA (testset)	other	0.00121	0.99879	other
CL2001032625AA	other	0.04004	0.95996	other
CL2001032627AA (testset)	other	0.00944	0.99056	other
CL2001032628AA	other	0.00132	0.99868	other
CL2001032629AA	CARCINOID	0.97315	0.02685	CARCINOID
CL2001032630AA	CARCINOID	0.9874	0.0126	CARCINOID
CL2001032632AA	other	0.03577	0.96423	other
CL2001032638AA (testset)	other	0.00168	0.99832	other
CL2001032640AA	other	0.0279	0.9721	other
CL2001032643AA	other	0.00053	0.99947	other
CL2001032644AA (testset)	other	0.01484	0.98516	other
CL2001032647AA	other	0.00081	0.99919	other
CL2001032701AA	other	0.00089	0.99911	other
CL2001032702AA (testset)	other	0.00034	0.99966	other
CL2001032703AA	other	0.00023	0.99977	other
CL2001032704AA (testset)	other	0.00105	0.99895	other
CL2001032706AA	other	0.00056	0.99944	other
CL2001032709AA	other	0.0012	0.9988	other
CL2001032716AA	other	0.00139	0.99861	other
CL2001032717AA (testset)	other	0.00337	0.99663	other
CL2001032718AA	other	0.02307	0.97693	other
CL2001032719AA (testset)	other	0.00078	0.99922	other
CL2001032720AA	other	0.09706	0.90294	other
CL2001032722AA	CARCINOID	0.9978	0.0022	CARCINOID
CL2001032724AA	other	0.00382	0.99618	other
CL2001032725AA (testset)	other	0.02878	0.97122	other
CL2001032727AA	other	0.032	0.968	other
CL2001032729AA (testset)	other	0.00026	0.99974	other
CL2001032730AA	other	0.00051	0.99949	other
CL2001032732AA (testset)	other	0.00149	0.99851	other
CL2001032733AA	other	0.01248	0.98752	other
CL2001032738AA	other	0.00014	0.99986	other
CL2001032742AA	other	0.00045	0.99955	other
CL2001032746AA	other	0.00058	0.99942	other
CL2001032747AA	other	0.01171	0.98829	other
CL2001032833AA	other	0.02132	0.97868	other
CL2001032836AA	other	5e-04	0.9995	other
CL2001032838AA	other	0.00278	0.99722	other
CL2001032839AA	other	0.00685	0.99315	other
CL2001032841AA	other	0.00437	0.99563	other
CL2001032842AA (testset)	other	0.00227	0.99773	other
CL2001032843AA (testset)	other	0.00219	0.99781	other
CL2001032845AA (testset)	other	0.0057	0.9943	other
CL2001032846AA	other	0.00457	0.99543	other
CL2001032847AA	CARCINOID	0.99638	0.00362	CARCINOID
CL2001032848AA (testset)	other	0.01233	0.98767	other
CL2001032850AA	CARCINOID	0.98605	0.01395	CARCINOID
CL2001032853AA (testset)	other	0.00731	0.99269	other
CL2001032854AA	CARCINOID	0.92572	0.07428	CARCINOID
CL2001032856AA	other	0.00186	0.99814	other
CL2001032857AA (testset)	other	0.00276	0.99724	other
CL2001032860AA	CARCINOID	0.99081	0.00919	CARCINOID
CL2001040305AA	other	0.00511	0.99489	other
CL2001040306AA	other	0.01335	0.98665	other
CL2001041708AA	other	0.00228	0.99772	other
CL2001041711AA (testset)	other	0.01047	0.98953	other
CL2001041716AA	other	0.00674	0.99326	other
CL2001042501AA (testset)	CARCINOID	0.96095	0.03905	CARCINOID
CL2001042505AA	other	0.02328	0.97672	other
CL2001042506AA	other	0.00287	0.99713	other