StAM Report: Prediction of NORMAL (predictive) - beta 0.081, 0.919

• 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:	135 ( 11 from NORMAL, 124 from other )
Test samples:	68 ( 6 from NORMAL, 62 from other )
Focus on class:	NORMAL
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:	135
Number of classes:	2
Class weights:	'NORMAL': 0.081 'other': 0.919
Class prior:	'NORMAL':0.081 'other':0.919
Shrinkage candidates:	0, 0.048, 0.096, 0.144, 0.192, 0.24, 0.287, 0.335, 0.383, 0.431, 0.479, 0.527, 0.575, 0.623, 0.671, 0.719, 0.767, 0.815, 0.862, 0.91, 0.958, 1.006, 1.054, 1.102, 1.15, 1.198, 1.246, 1.294, 1.342, 1.39

Cross validated performance

Download postscript

Download postscript

	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.01481	0.3595	1.9528	2203	8656
0.048	0.01481	0.35817	1.95295	2203	8656
0.096	0.01481	0.35671	1.95311	2203	8656
0.144	0.01481	0.3551	1.9533	2203	8656
0.192	0.01481	0.35331	1.9535	2203	8656
0.24	0.01481	0.35129	1.95373	2203	8656
0.287	0.01481	0.34903	1.95399	2203	8656
0.335	0.01481	0.34648	1.9543	2203	8656
0.383	0.01481	0.34358	1.95465	2203	8656
0.431	0.01481	0.34025	1.95506	2203	8656
0.479	0.01481	0.33638	1.95555	2203	8656
0.527	0.01481	0.33184	1.95614	2203	8656
0.575	0.01481	0.32643	1.95688	2203	8656
0.623	0.01481	0.31986	1.95782	2203	8656
0.671	0.01481	0.31175	1.95905	2203	8656
0.719	0.01481	0.30143	1.96074	2203	8656
0.767	0.01481	0.28786	1.96321	2203	8656
0.815	0.01481	0.26917	1.96718	2203	8656
0.862	0.01481	0.24167	1.97475	2203	8656
0.91	0.02222	0.19663	1.99594	2201	8575
0.958	0.02222	0.17938	2.81128	525	7740
1.006	0.02222	0.17767	2.81573	524	7739
1.054	0.02222	0.1752	2.83388	520	7731
1.102	0.01481	0.17137	2.90933	470	7574
1.15	0.00741	0.16553	2.96769	428	7468
1.198	0.00741	0.15861	3.10237	363	7282
1.246	0.00741	0.1496	3.21753	282	6648
1.294	0.01481	0.13816	3.34018	192	5203
1.342	0.01481	0.14864	3.2229	69	919

Information on Model Fit

Fit for D = 1.2458

Number of classes:	2
Class weights:	'NORMAL': 0.081 'other': 0.919
Class prior:	'NORMAL':0.081 'other':0.919
Chosen shrinkage level:	1.246 (by optimizing the root's error rate )
Number of nodes left	282
Number of accessible genes	6648

Shrunken prediction graph

Hover over a node to see its description, click on it to view its detailed results.

Download postscript

Nodewise evaluation

Download postscript

Information on Predictions

Number of samples:	203 (17 from NORMAL, 186 from other)
Test samples:	68 (6 from NORMAL, 62 from other)
Classes:	NORMAL, other

Illustration of Performance on testdata

Nodewise evaluation

Download postscript

Prediction image

Hover over a node description to see its ID, click on it to see detailed results.

Download postscript

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	0.09595
GO:0009987	cellular process	0.22166
GO:0007275	development	0.22557
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.23883
GO:0050789	regulation of biological process	0.21799
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0.01481
• Performance: 0.1496
• Redundancy: 3.01423

	Sensitivity	Specificity
NORMAL	0.90909	0.99194
other	0.99194	0.90909

Performance on test data

• Error rate: 0.01471
• Performance: 0.13673
• Redundancy: 2.97345

	Sensitivity	Specificity
NORMAL	0.83333	1
other	1	0.83333

Predictions

	Class	NORMAL	other	Predictionn
CL2001031606AA	other	0.00379	0.99621	other
CL2001031607AA	other	0.06634	0.93366	other
CL2001031608AA	other	0.04931	0.95069	other
CL2001031609AA	other	0.01553	0.98447	other
CL2001031611AA	other	0.01747	0.98253	other
CL2001031612AA	other	0.06772	0.93228	other
CL2001031613AA	other	0.18065	0.81935	other
CL2001031615AA	other	0.01107	0.98893	other
CL2001031616AA (testset)	other	0.02274	0.97726	other
CL2001031618AA	other	0.02661	0.97339	other
CL2001031620AA (testset)	other	0.01256	0.98744	other
CL2001031621AA (testset)	other	0.01661	0.98339	other
CL2001031622AA	other	0.00901	0.99099	other
CL2001031625AA	other	0.04057	0.95943	other
CL2001031627AA (testset)	other	0.03193	0.96807	other
CL2001031628AA (testset)	other	0.0269	0.9731	other
CL2001031629AA	other	0.01089	0.98911	other
CL2001031630AA (testset)	other	0.01035	0.98965	other
CL2001031631AA	other	0.01121	0.98879	other
CL2001031632AA	other	0.01261	0.98739	other
CL2001031634AA	other	0.03064	0.96936	other
CL2001031635AA	other	0.03104	0.96896	other
CL2001031636AA	other	0.01358	0.98642	other
CL2001032002AA	other	0.02409	0.97591	other
CL2001032005AA	other	0.00706	0.99294	other
CL2001032008AA	other	0.00823	0.99177	other
CL2001032009AA (testset)	other	0.01918	0.98082	other
CL2001032010AA (testset)	NORMAL	0.57385	0.42615	NORMAL
CL2001032011AA (testset)	other	0.08321	0.91679	other
CL2001032012AA (testset)	other	0.0664	0.9336	other
CL2001032013AA (testset)	other	0.05026	0.94974	other
CL2001032015AA	other	0.25556	0.74444	other
CL2001032016AA (testset)	other	0.02349	0.97651	other
CL2001032019AA	other	0.02761	0.97239	other
CL2001032020AA (testset)	other	0.02793	0.97207	other
CL2001032025AA	other	0.01943	0.98057	other
CL2001032026AA	other	0.01695	0.98305	other
CL2001032027AA	other	0.05048	0.94952	other
CL2001032030AA	other	0.01266	0.98734	other
CL2001032031AA (testset)	other	0.04818	0.95182	other
CL2001032032AA	other	0.05682	0.94318	other
CL2001032034AA	other	0.28921	0.71079	other
CL2001032036AA	other	0.06716	0.93284	other
CL2001032041AA	NORMAL	0.68512	0.31488	NORMAL
CL2001032043AA	NORMAL	0.91155	0.08845	NORMAL
CL2001032044AA	other	0.01578	0.98422	other
CL2001032045AA (testset)	NORMAL	0.71183	0.28817	NORMAL
CL2001032046AA	NORMAL	0.75482	0.24518	NORMAL
CL2001032101AA	other	0.0548	0.9452	other
CL2001032102AA	NORMAL	0.84891	0.15109	NORMAL
CL2001032103AA	other	0.01687	0.98313	other
CL2001032104AA	other	0.01683	0.98317	other
CL2001032105AA	other	0.00639	0.99361	other
CL2001032107AA	other	0.0093	0.9907	other
CL2001032108AA	other	0.03135	0.96865	other
CL2001032109AA (testset)	other	0.10608	0.89392	other
CL2001032110AA	other	0.07108	0.92892	other
CL2001032111AA	other	0.0373	0.9627	other
CL2001032113AA (testset)	other	0.00479	0.99521	other
CL2001032114AA	other	0.03084	0.96916	other
CL2001032115AA (testset)	other	0.01601	0.98399	other
CL2001032116AA (testset)	other	0.02293	0.97707	other
CL2001032117AA	other	0.0223	0.9777	other
CL2001032121AA	other	0.01135	0.98865	other
CL2001032122AA	other	0.01431	0.98569	other
CL2001032124AA	other	0.02457	0.97543	other
CL2001032125AA	other	0.01212	0.98788	other
CL2001032127AA (testset)	other	0.03197	0.96803	other
CL2001032128AA (testset)	NORMAL	0.77989	0.22011	NORMAL
CL2001032129AA (testset)	other	0.02695	0.97305	other
CL2001032130AA	other	0.02062	0.97938	other
CL2001032132AA	other	0.05844	0.94156	other
CL2001032134AA (testset)	other	0.1084	0.8916	other
CL2001032135AA	other	0.09257	0.90743	other
CL2001032136AA (testset)	other	0.03254	0.96746	other
CL2001032138AA (testset)	other	0.04505	0.95495	other
CL2001032141AA (testset)	other	0.02498	0.97502	other
CL2001032142AA	other	0.02166	0.97834	other
CL2001032144AA	other	0.0174	0.9826	other
CL2001032145AA	other	0.03677	0.96323	other
CL2001032147AA	NORMAL	0.87427	0.12573	NORMAL
CL2001032149AA (testset)	other	0.07437	0.92563	other
CL2001032151AA	other	0.00967	0.99033	other
CL2001032152AA	other	0.01751	0.98249	other
CL2001032153AA	other	0.07199	0.92801	other
CL2001032155AA	other	0.37651	0.62349	other
CL2001032156AA (testset)	other	0.09032	0.90968	other
CL2001032202AA (testset)	NORMAL	0.8751	0.1249	NORMAL
CL2001032206AA	NORMAL	0.71435	0.28565	NORMAL
CL2001032207AA	other	0.0155	0.9845	other
CL2001032209AA	other	0.01844	0.98156	other
CL2001032210AA	other	0.02621	0.97379	other
CL2001032211AA (testset)	other	0.00844	0.99156	other
CL2001032212AA	other	0.01199	0.98801	other
CL2001032213AA	other	0.09252	0.90748	other
CL2001032214AA (testset)	other	0.17981	0.82019	other
CL2001032217AA (testset)	other	0.00524	0.99476	other
CL2001032218AA	other	0.01283	0.98717	other
CL2001032219AA (testset)	other	0.03742	0.96258	other
CL2001032220AA	NORMAL	0.85884	0.14116	NORMAL
CL2001032222AA (testset)	other	0.01426	0.98574	other
CL2001032229AA (testset)	other	0.01848	0.98152	other
CL2001032231AA	other	0.03668	0.96332	other
CL2001032232AA	other	0.03853	0.96147	other
CL2001032233AA (testset)	other	0.01026	0.98974	other
CL2001032238AA	other	0.02254	0.97746	other
CL2001032239AA	other	0.02268	0.97732	other
CL2001032240AA	other	0.02197	0.97803	other
CL2001032241AA (testset)	other	0.05519	0.94481	other
CL2001032242AA	other	0.02125	0.97875	other
CL2001032243AA	other	0.05009	0.94991	other
CL2001032248AA	other	0.00678	0.99322	other
CL2001032249AA (testset)	other	0.04843	0.95157	other
CL2001032252AA (testset)	other	0.04446	0.95554	other
CL2001032254AA (testset)	other	0.02106	0.97894	other
CL2001032255AA	other	0.01396	0.98604	other
CL2001032256AA (testset)	NORMAL	0.32826	0.67174	other
CL2001032259AA (testset)	other	0.04163	0.95837	other
CL2001032260AA	other	0.06324	0.93676	other
CL2001032301AA	other	0.03176	0.96824	other
CL2001032304AA	NORMAL	0.56016	0.43984	NORMAL
CL2001032305AA (testset)	other	0.01903	0.98097	other
CL2001032306AA (testset)	other	0.0202	0.9798	other
CL2001032307AA (testset)	other	0.22406	0.77594	other
CL2001032308AA	other	0.0142	0.9858	other
CL2001032309AA	other	0.01405	0.98595	other
CL2001032310AA	other	0.01203	0.98797	other
CL2001032311AA (testset)	other	0.01359	0.98641	other
CL2001032312AA	other	0.01925	0.98075	other
CL2001032313AA (testset)	other	0.01353	0.98647	other
CL2001032314AA (testset)	other	0.00913	0.99087	other
CL2001032316AA	other	0.01936	0.98064	other
CL2001032601AA	other	0.00992	0.99008	other
CL2001032602AA	other	0.01505	0.98495	other
CL2001032604AA	other	0.02167	0.97833	other
CL2001032607AA	other	0.01109	0.98891	other
CL2001032608AA	other	0.02139	0.97861	other
CL2001032610AA	other	0.00892	0.99108	other
CL2001032612AA	other	0.02263	0.97737	other
CL2001032613AA (testset)	other	0.01258	0.98742	other
CL2001032614AA	other	0.00771	0.99229	other
CL2001032616AA	other	0.01908	0.98092	other
CL2001032617AA (testset)	other	0.01193	0.98807	other
CL2001032620AA (testset)	other	0.01617	0.98383	other
CL2001032625AA	other	0.00667	0.99333	other
CL2001032627AA	other	0.01211	0.98789	other
CL2001032628AA	other	0.01245	0.98755	other
CL2001032629AA	other	0.00493	0.99507	other
CL2001032630AA (testset)	other	0.03723	0.96277	other
CL2001032632AA	other	0.00649	0.99351	other
CL2001032638AA	other	0.02104	0.97896	other
CL2001032640AA (testset)	other	0.03027	0.96973	other
CL2001032643AA	other	0.01707	0.98293	other
CL2001032644AA (testset)	other	0.01429	0.98571	other
CL2001032647AA	other	0.07968	0.92032	other
CL2001032701AA	other	0.01934	0.98066	other
CL2001032702AA	other	0.0431	0.9569	other
CL2001032703AA	other	0.02412	0.97588	other
CL2001032704AA	other	0.04033	0.95967	other
CL2001032706AA (testset)	other	0.02775	0.97225	other
CL2001032709AA	other	0.02742	0.97258	other
CL2001032716AA	other	0.04039	0.95961	other
CL2001032717AA	other	0.0131	0.9869	other
CL2001032718AA (testset)	NORMAL	0.88641	0.11359	NORMAL
CL2001032719AA	other	0.03405	0.96595	other
CL2001032720AA	other	0.00367	0.99633	other
CL2001032722AA	other	0.02785	0.97215	other
CL2001032724AA	NORMAL	0.35894	0.64106	other
CL2001032725AA	NORMAL	0.83546	0.16454	NORMAL
CL2001032727AA	NORMAL	0.78515	0.21485	NORMAL
CL2001032729AA	other	0.01557	0.98443	other
CL2001032730AA (testset)	other	0.00693	0.99307	other
CL2001032732AA (testset)	other	0.0284	0.9716	other
CL2001032733AA	other	0.01721	0.98279	other
CL2001032738AA (testset)	other	0.01153	0.98847	other
CL2001032742AA (testset)	other	0.01051	0.98949	other
CL2001032746AA	other	0.01809	0.98191	other
CL2001032747AA	other	0.01618	0.98382	other
CL2001032833AA	other	0.02346	0.97654	other
CL2001032836AA (testset)	other	0.00761	0.99239	other
CL2001032838AA (testset)	other	0.03266	0.96734	other
CL2001032839AA	other	0.02414	0.97586	other
CL2001032841AA	other	0.03532	0.96468	other
CL2001032842AA	other	0.00712	0.99288	other
CL2001032843AA (testset)	other	0.01056	0.98944	other
CL2001032845AA (testset)	other	0.03557	0.96443	other
CL2001032846AA	other	0.04279	0.95721	other
CL2001032847AA	other	0.08408	0.91592	other
CL2001032848AA	other	0.76385	0.23615	NORMAL
CL2001032850AA	other	0.01684	0.98316	other
CL2001032853AA	other	0.02538	0.97462	other
CL2001032854AA (testset)	other	0.01222	0.98778	other
CL2001032856AA	other	0.02197	0.97803	other
CL2001032857AA	other	0.03136	0.96864	other
CL2001032860AA (testset)	other	0.01094	0.98906	other
CL2001040305AA	other	0.01122	0.98878	other
CL2001040306AA	other	0.02372	0.97628	other
CL2001041708AA	other	0.01097	0.98903	other
CL2001041711AA	other	0.02938	0.97062	other
CL2001041716AA	other	0.07628	0.92372	other
CL2001042501AA (testset)	other	0.00681	0.99319	other
CL2001042505AA	other	0.02308	0.97692	other
CL2001042506AA (testset)	other	0.0838	0.9162	other