StAM Report: Prediction of SQUAMOUS (predictive) - beta 0.104, 0.896

• 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 ( 14 from SQUAMOUS, 121 from other )
Test samples:	68 ( 7 from SQUAMOUS, 61 from other )
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:	135
Number of classes:	2
Class weights:	'SQUAMOUS': 0.104 'other': 0.896
Class prior:	'SQUAMOUS':0.104 'other':0.896
Shrinkage candidates:	0, 0.026, 0.053, 0.079, 0.105, 0.132, 0.158, 0.184, 0.211, 0.237, 0.264, 0.29, 0.316, 0.343, 0.369, 0.395, 0.422, 0.448, 0.474, 0.501, 0.527, 0.553, 0.58, 0.606, 0.633, 0.659, 0.685, 0.712, 0.738, 0.764

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.01481	0.46262	1.72561	2203	8431
0.026	0.01481	0.45067	1.72668	2203	8431
0.053	0.01481	0.43529	1.7281	2203	8431
0.079	0.01481	0.41554	1.73008	2203	8431
0.105	0.01481	0.38968	1.73301	2203	8431
0.132	0.01481	0.35463	1.73786	2203	8431
0.158	0.01481	0.30448	1.74765	2203	8431
0.184	0.01481	0.25012	2.35682	519	7537
0.211	0.01481	0.24715	2.36032	519	7537
0.237	0.01481	0.24349	2.38351	509	7534
0.264	0.01481	0.2391	2.39779	501	7478
0.29	0.01481	0.23367	2.41576	492	7445
0.316	0.01481	0.22704	2.4446	475	7432
0.343	0.01481	0.21895	2.51752	435	7401
0.369	0.01481	0.20816	2.59924	399	7348
0.395	0.00741	0.19515	2.66164	366	7131
0.422	0.00741	0.18229	2.75191	326	6937
0.448	0.00741	0.1738	2.89565	283	6718
0.474	0.00741	0.16864	2.98957	253	6532
0.501	0.00741	0.16575	3.11271	226	6350
0.527	0.01481	0.1625	3.18834	188	5869
0.553	0.01481	0.15835	3.26131	155	5224
0.58	0.00741	0.15491	3.55059	118	4581
0.606	0.00741	0.14395	3.68772	90	3961
0.633	0.00741	0.13602	4.23896	61	1763
0.659	0.00741	0.15092	4.44568	48	1341
0.685	0.02222	0.15637	4.10604	37	695
0.712	0.02222	0.13462	4.50073	17	424
0.738	0.03704	0.1114	8.6746	6	336

Information on Model Fit

Fit for D = 0.6062

Number of classes:	2
Class weights:	'SQUAMOUS': 0.104 'other': 0.896
Class prior:	'SQUAMOUS':0.104 'other':0.896
Chosen shrinkage level:	0.606 (by optimizing the root's error rate )
Number of nodes left	90
Number of accessible genes	3961

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 (21 from SQUAMOUS, 182 from other)
Test samples:	68 (7 from SQUAMOUS, 61 from other)
Classes:	SQUAMOUS, 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	0.3062
GO:0007275	development	0.33755
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.35625
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0.00741
• Performance: 0.14395
• Redundancy: 3.55041

	Sensitivity	Specificity
SQUAMOUS	0.92857	1
other	1	0.92857

Performance on test data

• Error rate: 0.01471
• Performance: 0.1329
• Redundancy: 3.77861

	Sensitivity	Specificity
SQUAMOUS	0.85714	1
other	1	0.85714

Predictions

	Class	SQUAMOUS	other	Predictionn
CL2001031606AA (testset)	SQUAMOUS	0.58388	0.41612	SQUAMOUS
CL2001031607AA	other	0.01814	0.98186	other
CL2001031608AA	other	0.00321	0.99679	other
CL2001031609AA (testset)	other	0.00301	0.99699	other
CL2001031611AA	other	0.0403	0.9597	other
CL2001031612AA (testset)	other	0.22194	0.77806	other
CL2001031613AA (testset)	other	0.13689	0.86311	other
CL2001031615AA (testset)	other	0.03362	0.96638	other
CL2001031616AA	other	0.11834	0.88166	other
CL2001031618AA	other	0.00088	0.99912	other
CL2001031620AA	SQUAMOUS	0.74575	0.25425	SQUAMOUS
CL2001031621AA	SQUAMOUS	0.90476	0.09524	SQUAMOUS
CL2001031622AA	other	0.38556	0.61444	other
CL2001031625AA	other	0.0021	0.9979	other
CL2001031627AA (testset)	other	0.00799	0.99201	other
CL2001031628AA	other	0.00467	0.99533	other
CL2001031629AA	other	0.32187	0.67813	other
CL2001031630AA	other	0.00078	0.99922	other
CL2001031631AA (testset)	other	0.02971	0.97029	other
CL2001031632AA	other	0.04988	0.95012	other
CL2001031634AA	other	0.00346	0.99654	other
CL2001031635AA (testset)	other	0.00174	0.99826	other
CL2001031636AA (testset)	other	0.20948	0.79052	other
CL2001032002AA	other	0.00111	0.99889	other
CL2001032005AA	other	0.00479	0.99521	other
CL2001032008AA	other	0.05701	0.94299	other
CL2001032009AA	other	0.00726	0.99274	other
CL2001032010AA	other	0.0024	0.9976	other
CL2001032011AA	other	0.00688	0.99312	other
CL2001032012AA	other	0.00138	0.99862	other
CL2001032013AA	other	0.00349	0.99651	other
CL2001032015AA (testset)	other	0.01376	0.98624	other
CL2001032016AA (testset)	other	0.00282	0.99718	other
CL2001032019AA	other	0.00779	0.99221	other
CL2001032020AA (testset)	other	0.01167	0.98833	other
CL2001032025AA (testset)	other	0.00502	0.99498	other
CL2001032026AA	other	0.00565	0.99435	other
CL2001032027AA (testset)	other	0.03883	0.96117	other
CL2001032030AA (testset)	other	0.04023	0.95977	other
CL2001032031AA (testset)	other	0.01067	0.98933	other
CL2001032032AA	other	0.00157	0.99843	other
CL2001032034AA (testset)	other	0.024	0.976	other
CL2001032036AA	other	0.28964	0.71036	other
CL2001032041AA (testset)	other	0.03823	0.96177	other
CL2001032043AA	other	0.00975	0.99025	other
CL2001032044AA	other	0.00074	0.99926	other
CL2001032045AA (testset)	other	0.00225	0.99775	other
CL2001032046AA	other	0.00245	0.99755	other
CL2001032101AA	other	0.01363	0.98637	other
CL2001032102AA	other	0.00554	0.99446	other
CL2001032103AA	other	0.00159	0.99841	other
CL2001032104AA	other	0.02836	0.97164	other
CL2001032105AA	other	0.01162	0.98838	other
CL2001032107AA	other	0.00354	0.99646	other
CL2001032108AA (testset)	other	0.00174	0.99826	other
CL2001032109AA (testset)	other	0.00116	0.99884	other
CL2001032110AA	other	0.00616	0.99384	other
CL2001032111AA (testset)	other	0.00301	0.99699	other
CL2001032113AA	other	0.00298	0.99702	other
CL2001032114AA	other	0.00373	0.99627	other
CL2001032115AA	other	0.00107	0.99893	other
CL2001032116AA	other	0.00362	0.99638	other
CL2001032117AA (testset)	other	0.02229	0.97771	other
CL2001032121AA	other	0.01847	0.98153	other
CL2001032122AA	SQUAMOUS	0.81979	0.18021	SQUAMOUS
CL2001032124AA (testset)	other	0.00361	0.99639	other
CL2001032125AA	other	0.07335	0.92665	other
CL2001032127AA (testset)	other	0.00564	0.99436	other
CL2001032128AA (testset)	other	0.03059	0.96941	other
CL2001032129AA (testset)	SQUAMOUS	0.96278	0.03722	SQUAMOUS
CL2001032130AA	other	0.02781	0.97219	other
CL2001032132AA (testset)	other	0.00311	0.99689	other
CL2001032134AA	other	0.05871	0.94129	other
CL2001032135AA	other	0.0377	0.9623	other
CL2001032136AA (testset)	other	0.06029	0.93971	other
CL2001032138AA	other	0.00742	0.99258	other
CL2001032141AA	other	0.03811	0.96189	other
CL2001032142AA	other	0.12775	0.87225	other
CL2001032144AA	SQUAMOUS	0.94562	0.05438	SQUAMOUS
CL2001032145AA (testset)	other	0.00184	0.99816	other
CL2001032147AA (testset)	other	0.01226	0.98774	other
CL2001032149AA (testset)	other	0.09904	0.90096	other
CL2001032151AA (testset)	other	0.00192	0.99808	other
CL2001032152AA	other	0.00123	0.99877	other
CL2001032153AA (testset)	SQUAMOUS	0.64345	0.35655	SQUAMOUS
CL2001032155AA	other	0.22213	0.77787	other
CL2001032156AA	other	0.02098	0.97902	other
CL2001032202AA	other	0.00872	0.99128	other
CL2001032206AA (testset)	other	0.02034	0.97966	other
CL2001032207AA	SQUAMOUS	0.93022	0.06978	SQUAMOUS
CL2001032209AA (testset)	SQUAMOUS	0.96371	0.03629	SQUAMOUS
CL2001032210AA	other	0.00453	0.99547	other
CL2001032211AA (testset)	other	0.02183	0.97817	other
CL2001032212AA (testset)	other	0.01926	0.98074	other
CL2001032213AA	other	0.02746	0.97254	other
CL2001032214AA	other	0.07285	0.92715	other
CL2001032217AA (testset)	other	0.00634	0.99366	other
CL2001032218AA	SQUAMOUS	0.8691	0.1309	SQUAMOUS
CL2001032219AA	other	0.00758	0.99242	other
CL2001032220AA	other	0.00123	0.99877	other
CL2001032222AA	SQUAMOUS	0.66276	0.33724	SQUAMOUS
CL2001032229AA	other	0.01044	0.98956	other
CL2001032231AA	SQUAMOUS	0.5554	0.4446	SQUAMOUS
CL2001032232AA (testset)	other	0.00257	0.99743	other
CL2001032233AA	other	0.00827	0.99173	other
CL2001032238AA (testset)	other	0.00079	0.99921	other
CL2001032239AA	SQUAMOUS	0.85015	0.14985	SQUAMOUS
CL2001032240AA	SQUAMOUS	0.93374	0.06626	SQUAMOUS
CL2001032241AA	other	0.00452	0.99548	other
CL2001032242AA	other	0.02478	0.97522	other
CL2001032243AA (testset)	other	0.00158	0.99842	other
CL2001032248AA	other	0.03003	0.96997	other
CL2001032249AA	other	0.00228	0.99772	other
CL2001032252AA	other	0.39192	0.60808	other
CL2001032254AA (testset)	other	0.00277	0.99723	other
CL2001032255AA (testset)	other	0.01133	0.98867	other
CL2001032256AA	other	0.0081	0.9919	other
CL2001032259AA (testset)	other	0.00876	0.99124	other
CL2001032260AA (testset)	other	0.00471	0.99529	other
CL2001032301AA	other	0.05837	0.94163	other
CL2001032304AA	other	0.01973	0.98027	other
CL2001032305AA (testset)	SQUAMOUS	0.31725	0.68275	other
CL2001032306AA	other	0.04414	0.95586	other
CL2001032307AA	other	0.0172	0.9828	other
CL2001032308AA	other	0.04462	0.95538	other
CL2001032309AA	other	0.00148	0.99852	other
CL2001032310AA	other	0.00712	0.99288	other
CL2001032311AA	other	0.11664	0.88336	other
CL2001032312AA	other	0.00373	0.99627	other
CL2001032313AA	other	0.00826	0.99174	other
CL2001032314AA	other	0.00164	0.99836	other
CL2001032316AA	other	0.00832	0.99168	other
CL2001032601AA	other	0.02147	0.97853	other
CL2001032602AA (testset)	other	0.00549	0.99451	other
CL2001032604AA (testset)	other	0.00749	0.99251	other
CL2001032607AA (testset)	other	0.00376	0.99624	other
CL2001032608AA	SQUAMOUS	0.9579	0.0421	SQUAMOUS
CL2001032610AA	other	0.01692	0.98308	other
CL2001032612AA	other	0.00721	0.99279	other
CL2001032613AA	other	0.00871	0.99129	other
CL2001032614AA (testset)	other	0.00478	0.99522	other
CL2001032616AA	other	0.00154	0.99846	other
CL2001032617AA	other	0.04835	0.95165	other
CL2001032620AA	other	0.00378	0.99622	other
CL2001032625AA	other	0.002	0.998	other
CL2001032627AA	SQUAMOUS	0.97858	0.02142	SQUAMOUS
CL2001032628AA	other	0.00599	0.99401	other
CL2001032629AA (testset)	other	0.00059	0.99941	other
CL2001032630AA (testset)	other	0.00433	0.99567	other
CL2001032632AA	other	0.04424	0.95576	other
CL2001032638AA	other	0.02927	0.97073	other
CL2001032640AA	other	0.00305	0.99695	other
CL2001032643AA	other	0.04799	0.95201	other
CL2001032644AA (testset)	SQUAMOUS	0.78051	0.21949	SQUAMOUS
CL2001032647AA	other	0.00552	0.99448	other
CL2001032701AA	other	0.00674	0.99326	other
CL2001032702AA	other	0.03637	0.96363	other
CL2001032703AA	other	0.14587	0.85413	other
CL2001032704AA	other	0.02766	0.97234	other
CL2001032706AA	other	0.01101	0.98899	other
CL2001032709AA (testset)	other	0.0157	0.9843	other
CL2001032716AA	other	0.08714	0.91286	other
CL2001032717AA (testset)	other	0.00439	0.99561	other
CL2001032718AA	other	0.03946	0.96054	other
CL2001032719AA (testset)	SQUAMOUS	0.81978	0.18022	SQUAMOUS
CL2001032720AA	other	0.03375	0.96625	other
CL2001032722AA	other	0.00522	0.99478	other
CL2001032724AA	other	0.00244	0.99756	other
CL2001032725AA (testset)	other	0.00238	0.99762	other
CL2001032727AA	other	0.00591	0.99409	other
CL2001032729AA	other	0.00777	0.99223	other
CL2001032730AA	other	0.0048	0.9952	other
CL2001032732AA	SQUAMOUS	0.29231	0.70769	other
CL2001032733AA (testset)	other	0.00811	0.99189	other
CL2001032738AA	other	0.04315	0.95685	other
CL2001032742AA (testset)	other	0.18021	0.81979	other
CL2001032746AA (testset)	other	0.04033	0.95967	other
CL2001032747AA (testset)	other	0.01202	0.98798	other
CL2001032833AA (testset)	other	0.01147	0.98853	other
CL2001032836AA	other	0.15432	0.84568	other
CL2001032838AA	other	0.02031	0.97969	other
CL2001032839AA	other	0.00775	0.99225	other
CL2001032841AA	other	0.00261	0.99739	other
CL2001032842AA	other	0.01554	0.98446	other
CL2001032843AA	other	0.00707	0.99293	other
CL2001032845AA (testset)	other	0.00225	0.99775	other
CL2001032846AA (testset)	other	0.00753	0.99247	other
CL2001032847AA (testset)	other	0.0021	0.9979	other
CL2001032848AA	other	0.03334	0.96666	other
CL2001032850AA	other	0.00117	0.99883	other
CL2001032853AA	SQUAMOUS	0.9391	0.0609	SQUAMOUS
CL2001032854AA	other	0.00154	0.99846	other
CL2001032856AA	other	0.00819	0.99181	other
CL2001032857AA	other	0.00102	0.99898	other
CL2001032860AA	other	0.0053	0.9947	other
CL2001040305AA	other	0.042	0.958	other
CL2001040306AA	other	0.00413	0.99587	other
CL2001041708AA (testset)	other	0.19111	0.80889	other
CL2001041711AA	other	0.00143	0.99857	other
CL2001041716AA	other	0.00663	0.99337	other
CL2001042501AA	other	0.00066	0.99934	other
CL2001042505AA (testset)	other	0.04966	0.95034	other
CL2001042506AA	other	0.01722	0.98278	other