StAM Report: Prediction of recurred (predictive) - beta 0.657, 0.343

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

Information on Evaluation

Total number of samples:	52
Training samples:	35 ( 23 from not.recurred, 12 from recurred )
Test samples:	17 ( 11 from not.recurred, 6 from recurred )
Focus on class:	recurred
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:	35
Number of classes:	2
Class weights:	'not.recurred': 0.657 'recurred': 0.343
Class prior:	'not.recurred':0.657 'recurred':0.343
Shrinkage candidates:	0, 0.031, 0.062, 0.093, 0.125, 0.156, 0.187, 0.218, 0.249, 0.28, 0.311, 0.343, 0.374, 0.405, 0.436, 0.467, 0.498, 0.529, 0.56, 0.592, 0.623, 0.654, 0.685, 0.716, 0.747, 0.778, 0.81, 0.841, 0.872, 0.903

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.17143	0.91799	0.82344	2203	8634
0.031	0.17143	0.90561	0.82445	2203	8634
0.062	0.17143	0.89123	0.82589	2203	8634
0.093	0.17143	0.87369	0.82818	2203	8634
0.125	0.17143	0.84681	0.83264	2203	8634
0.156	0.17143	0.83574	0.90282	1192	8388
0.187	0.17143	0.82529	0.90801	1171	8386
0.218	0.17143	0.81542	0.91504	1128	8050
0.249	0.17143	0.80392	0.92761	1053	8033
0.28	0.17143	0.79131	0.9482	942	7999
0.311	0.14286	0.77824	0.96152	864	7862
0.343	0.14286	0.7666	0.97993	772	7818
0.374	0.14286	0.7558	1.00093	688	7738
0.405	0.14286	0.7453	1.01173	611	7645
0.436	0.17143	0.74019	1.03084	511	7390
0.467	0.17143	0.73319	1.08583	401	7119
0.498	0.14286	0.72836	1.11235	333	6823
0.529	0.14286	0.72383	1.14419	277	6435
0.56	0.14286	0.71488	1.13528	245	5794
0.592	0.14286	0.69976	1.19397	177	5325
0.623	0.14286	0.68234	1.17707	143	4674
0.654	0.08571	0.66022	1.27129	95	4027
0.685	0.17143	0.64112	1.38497	69	3424
0.716	0.14286	0.62581	1.6927	50	2845
0.747	0.17143	0.61248	1.70553	48	2306
0.778	0.17143	0.60216	1.65604	47	2251
0.81	0.14286	0.59098	1.63468	40	1143
0.841	0.14286	0.58377	1.68499	32	875
0.872	0.05714	1.0635	1.18898	25	516

Information on Model Fit

Fit for D = 0.8718

Number of classes:	2
Class weights:	'not.recurred': 0.657 'recurred': 0.343
Class prior:	'not.recurred':0.657 'recurred':0.343
Chosen shrinkage level:	0.872 (by optimizing the root's error rate )
Number of nodes left	25
Number of accessible genes	516

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:	52 (34 from not.recurred, 18 from recurred)
Test samples:	17 (11 from not.recurred, 6 from recurred)
Classes:	not.recurred, recurred

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	0.45206
GO:0007275	development	0.15776
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.39017
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0.31429
• Performance: 1.06349
• Redundancy: 1.17831

	Sensitivity	Specificity
not.recurred	0.91304	0.25
recurred	0.25	0.91304

Performance on test data

• Error rate: 0.17647
• Performance: 0.97874
• Redundancy: 1.65852

	Sensitivity	Specificity
not.recurred	0.90909	0.66667
recurred	0.66667	0.90909

Predictions

	Class	not.recurred	recurred	Predictionn
0029_1222_H95A2_KF0146 (testset)	recurred	0.28903	0.71097	recurred
0029_1224_HU95A_KF0150	recurred	0.24553	0.75447	recurred
0029_1237_H95A2_KF0125	not.recurred	0.41628	0.58372	recurred
0029_1238_H95A2_KF0128	recurred	0.26721	0.73279	recurred
0029_1239_H95A2_KF0131	recurred	0.38119	0.61881	recurred
0029_1240_H95A2_KF0133	recurred	0.05897	0.94103	recurred
0029_1241_H95A2_KF0142	recurred	0.4392	0.5608	recurred
0029_1242_H95A2_KF0149 (testset)	recurred	0.34696	0.65304	recurred
0029_1243_H95A2_KF0154	recurred	0.02994	0.97006	recurred
0029_1244_H95A2_KF0153 (testset)	recurred	0.21523	0.78477	recurred
0029_1245_H95A2_KF0140 (testset)	recurred	0.02453	0.97547	recurred
0029_1246_H95A2_KF0139 (testset)	not.recurred	0.02809	0.97191	recurred
0029_1247_H95A2_KF0138	recurred	0.00263	0.99737	recurred
0029_1248_H95A2_KF0135	recurred	0.0219	0.9781	recurred
0029_1249_H95A2_KF0134	recurred	0.00834	0.99166	recurred
0029_1250_H95A2_KF0129	not.recurred	0.89578	0.10422	not.recurred
0029_1344_H95A2_KF-188	recurred	0.59109	0.40891	not.recurred
0029_1353_H95A2_KF-176	recurred	0.72727	0.27273	not.recurred
0029_1355_H95A2_KF-182 (testset)	not.recurred	0.78389	0.21611	not.recurred
0029_1357_H95A2_KF-187	recurred	0.59003	0.40997	not.recurred
0029_1397_H95A2_KF-207	not.recurred	0.85175	0.14825	not.recurred
0029_1398_H95A2_KF-193 (testset)	recurred	0.68056	0.31944	not.recurred
0029_1399_H95A2_KF-200 (testset)	recurred	0.65458	0.34542	not.recurred
0029_1425_H95A2_T96-159 (testset)	not.recurred	0.68967	0.31033	not.recurred
0029_1426_H95A2_T96-167 (testset)	not.recurred	0.89025	0.10975	not.recurred
0029_1427_H95A2_T96-195	not.recurred	0.94787	0.05213	not.recurred
0029_1428_H95A2_T96-250	not.recurred	0.85813	0.14187	not.recurred
0029_1429_H95A2_T97-017 (testset)	not.recurred	0.89967	0.10033	not.recurred
0029_1430_H95A2_T97-019 (testset)	not.recurred	0.9885	0.0115	not.recurred
0029_1431_H95A2_T97-043 (testset)	not.recurred	0.86615	0.13385	not.recurred
0029_1434_H95A2_T97-071	not.recurred	0.48004	0.51996	recurred
0029_1435_H95A2_T97-0075	not.recurred	0.97543	0.02457	not.recurred
0029_1436_H95A2_T97-0080 (testset)	not.recurred	0.76895	0.23105	not.recurred
0029_1437_H95A2_T97-0090 (testset)	not.recurred	0.95846	0.04154	not.recurred
0029_1438_H95A2_T97-0094	not.recurred	0.96283	0.03717	not.recurred
0029_1455_H95A2_T97-191	not.recurred	0.98288	0.01712	not.recurred
0029_1457_H95A2_T97-281 (testset)	not.recurred	0.91371	0.08629	not.recurred
0029_1461_H95A2_T92-37	not.recurred	0.97845	0.02155	not.recurred
0029_1464_H95A2_T92-58	not.recurred	0.92989	0.07011	not.recurred
0029_1469_H95A2_T94-71	not.recurred	0.91898	0.08102	not.recurred
0029_1470_H95A2_T94-72	not.recurred	0.87623	0.12377	not.recurred
0029_1471_H95A2_T94-74	not.recurred	0.85272	0.14728	not.recurred
0029_1473_H95A2_T95-28	not.recurred	0.86574	0.13426	not.recurred
0029_1474_H95A2_T95-31	not.recurred	0.97431	0.02569	not.recurred
0029_1475_H95A2_T95-40	not.recurred	0.76476	0.23524	not.recurred
0029_1476_H95A2_T95-74	not.recurred	0.84135	0.15865	not.recurred
0029_1479_H95A2_T95-162	not.recurred	0.9741	0.0259	not.recurred
0029_1481_H95A2_T95-194	not.recurred	0.87173	0.12827	not.recurred
0029_1482_H95A2_T96-85 (testset)	not.recurred	0.87461	0.12539	not.recurred
0029_1483_H95A2_T96-94	not.recurred	0.77452	0.22548	not.recurred
0029_1485_H95A2_T96-136	not.recurred	0.97035	0.02965	not.recurred
0029_1486_H95A2_T93-2	not.recurred	0.99241	0.00759	not.recurred