StAM Report: Prediction of recurred (explorative) - beta 0.1, 0.9

• 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:	52 ( 34 from not.recurred, 18 from recurred )
Test samples:	52 ( 34 from not.recurred, 18 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:	52
Number of classes:	2
Class weights:	'not.recurred': 0.1 'recurred': 0.9
Class prior:	'not.recurred':0.654 'recurred':0.346
Shrinkage candidates:	0, 0.085, 0.169, 0.254, 0.338, 0.423, 0.507, 0.592, 0.676, 0.761, 0.845, 0.93, 1.014, 1.099, 1.183, 1.268, 1.353, 1.437, 1.522, 1.606, 1.691, 1.775, 1.86, 1.944, 2.029, 2.113, 2.198, 2.282, 2.367, 2.452

Cross validated performance

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	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.13462	1.63713	0.81331	2203	8626
0.085	0.13462	1.63425	0.81339	2203	8626
0.169	0.13462	1.63103	0.81347	2203	8626
0.254	0.13462	1.62737	0.81339	2202	8618
0.338	0.13462	1.62323	0.81332	2201	8551
0.423	0.15385	1.61851	0.81327	2200	8528
0.507	0.15385	1.6131	0.81342	2200	8528
0.592	0.15385	1.60683	0.81359	2200	8528
0.676	0.15385	1.59947	0.81363	2199	8520
0.761	0.15385	1.59072	0.81389	2199	8520
0.845	0.15385	1.58014	0.81421	2199	8520
0.93	0.15385	1.56711	0.81462	2199	8520
1.014	0.15385	1.55067	0.81503	2198	8506
1.099	0.15385	1.52926	0.81585	2198	8506
1.183	0.15385	1.50018	0.81715	2198	8506
1.268	0.15385	1.45802	0.81938	2197	8490
1.353	0.15385	1.39656	0.87904	1245	8243
1.437	0.15385	1.36139	0.89194	1167	8226
1.522	0.17308	1.30975	0.91536	1004	8173
1.606	0.15385	1.26302	0.97578	716	8011
1.691	0.15385	1.22771	1.03578	549	7820
1.775	0.15385	1.19334	1.10296	420	7554
1.86	0.15385	1.18582	1.1644	326	7062
1.944	0.11538	1.18387	1.18261	257	6449
2.029	0.09615	1.16157	1.27416	159	5871
2.113	0.07692	1.12983	1.35263	104	3708
2.198	0.09615	1.08238	1.35743	77	3114
2.282	0.11538	1.04242	1.36614	39	1605
2.367	0.13462	1.54507	1.45808	15	508

Information on Model Fit

Performance vs. redundancy

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	Best Delta	Root Error Rate	Performance	Redundancy	#Nodes	#Genes
0	0.4227	0.1538	1.6185	0.8133	2200	8528
0.1	1.268	0.1538	1.458	0.8194	2197	8490
0.2	1.268	0.1538	1.458	0.8194	2197	8490
0.3	1.268	0.1538	1.458	0.8194	2197	8490
0.4	1.5216	0.1731	1.3098	0.9154	1004	8173
0.5	1.5216	0.1731	1.3098	0.9154	1004	8173
0.6	1.6062	0.1538	1.263	0.9758	716	8011
0.7	2.2824	0.1154	1.0424	1.3661	39	1605
0.8	2.2824	0.1154	1.0424	1.3661	39	1605
0.9	2.2824	0.1154	1.0424	1.3661	39	1605
1	2.2824	0.1154	1.0424	1.3661	39	1605

Fit for D = 2.2824

Number of classes:	2
Class weights:	'not.recurred': 0.1 'recurred': 0.9
Class prior:	'not.recurred':0.654 'recurred':0.346
Chosen shrinkage level:	2.282 (by accepting the system default (after consulting weighting alternatives) )
Number of nodes left	39
Number of accessible genes	1605

Shrunken prediction graph

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Nodewise evaluation

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Information on Predictions

Number of samples:	52 (34 from not.recurred, 18 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	0.413
GO:0007275	development	0.00000
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	0.587
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0.11538
• Performance: 1.04243
• Redundancy: 1.49991

	Sensitivity	Specificity
not.recurred	0.94118	0.77778
recurred	0.77778	0.94118

Performance on test data

• Error rate: 0.11538
• Performance: 0.81905
• Redundancy: 1.71369

	Sensitivity	Specificity
not.recurred	0.94118	0.77778
recurred	0.77778	0.94118

Predictions

	Class	not.recurred	recurred	Predictionn
0029_1222_H95A2_KF0146 (testset)	recurred	0.26575	0.73425	recurred
0029_1224_HU95A_KF0150 (testset)	recurred	0.63601	0.36399	not.recurred
0029_1237_H95A2_KF0125 (testset)	not.recurred	0.58508	0.41492	not.recurred
0029_1238_H95A2_KF0128 (testset)	recurred	0.14734	0.85266	recurred
0029_1239_H95A2_KF0131 (testset)	recurred	0.28113	0.71887	recurred
0029_1240_H95A2_KF0133 (testset)	recurred	0.17613	0.82387	recurred
0029_1241_H95A2_KF0142 (testset)	recurred	0.34786	0.65214	recurred
0029_1242_H95A2_KF0149 (testset)	recurred	0.21524	0.78476	recurred
0029_1243_H95A2_KF0154 (testset)	recurred	0.09428	0.90572	recurred
0029_1244_H95A2_KF0153 (testset)	recurred	0.07476	0.92524	recurred
0029_1245_H95A2_KF0140 (testset)	recurred	0.01625	0.98375	recurred
0029_1246_H95A2_KF0139 (testset)	not.recurred	0.07459	0.92541	recurred
0029_1247_H95A2_KF0138 (testset)	recurred	0.01598	0.98402	recurred
0029_1248_H95A2_KF0135 (testset)	recurred	0.03143	0.96857	recurred
0029_1249_H95A2_KF0134 (testset)	recurred	0.02105	0.97895	recurred
0029_1250_H95A2_KF0129 (testset)	not.recurred	0.86617	0.13383	not.recurred
0029_1344_H95A2_KF-188 (testset)	recurred	0.81194	0.18806	not.recurred
0029_1353_H95A2_KF-176 (testset)	recurred	0.80524	0.19476	not.recurred
0029_1355_H95A2_KF-182 (testset)	not.recurred	0.91867	0.08133	not.recurred
0029_1357_H95A2_KF-187 (testset)	recurred	0.50826	0.49174	not.recurred
0029_1397_H95A2_KF-207 (testset)	not.recurred	0.67037	0.32963	not.recurred
0029_1398_H95A2_KF-193 (testset)	recurred	0.40828	0.59172	recurred
0029_1399_H95A2_KF-200 (testset)	recurred	0.21546	0.78454	recurred
0029_1425_H95A2_T96-159 (testset)	not.recurred	0.77564	0.22436	not.recurred
0029_1426_H95A2_T96-167 (testset)	not.recurred	0.96882	0.03118	not.recurred
0029_1427_H95A2_T96-195 (testset)	not.recurred	0.96271	0.03729	not.recurred
0029_1428_H95A2_T96-250 (testset)	not.recurred	0.75664	0.24336	not.recurred
0029_1429_H95A2_T97-017 (testset)	not.recurred	0.89971	0.10029	not.recurred
0029_1430_H95A2_T97-019 (testset)	not.recurred	0.98715	0.01285	not.recurred
0029_1431_H95A2_T97-043 (testset)	not.recurred	0.96398	0.03602	not.recurred
0029_1434_H95A2_T97-071 (testset)	not.recurred	0.46007	0.53993	recurred
0029_1435_H95A2_T97-0075 (testset)	not.recurred	0.97286	0.02714	not.recurred
0029_1436_H95A2_T97-0080 (testset)	not.recurred	0.82724	0.17276	not.recurred
0029_1437_H95A2_T97-0090 (testset)	not.recurred	0.97601	0.02399	not.recurred
0029_1438_H95A2_T97-0094 (testset)	not.recurred	0.96476	0.03524	not.recurred
0029_1455_H95A2_T97-191 (testset)	not.recurred	0.96512	0.03488	not.recurred
0029_1457_H95A2_T97-281 (testset)	not.recurred	0.90726	0.09274	not.recurred
0029_1461_H95A2_T92-37 (testset)	not.recurred	0.96252	0.03748	not.recurred
0029_1464_H95A2_T92-58 (testset)	not.recurred	0.89267	0.10733	not.recurred
0029_1469_H95A2_T94-71 (testset)	not.recurred	0.91627	0.08373	not.recurred
0029_1470_H95A2_T94-72 (testset)	not.recurred	0.74284	0.25716	not.recurred
0029_1471_H95A2_T94-74 (testset)	not.recurred	0.77241	0.22759	not.recurred
0029_1473_H95A2_T95-28 (testset)	not.recurred	0.73501	0.26499	not.recurred
0029_1474_H95A2_T95-31 (testset)	not.recurred	0.97223	0.02777	not.recurred
0029_1475_H95A2_T95-40 (testset)	not.recurred	0.81098	0.18902	not.recurred
0029_1476_H95A2_T95-74 (testset)	not.recurred	0.72348	0.27652	not.recurred
0029_1479_H95A2_T95-162 (testset)	not.recurred	0.95883	0.04117	not.recurred
0029_1481_H95A2_T95-194 (testset)	not.recurred	0.80271	0.19729	not.recurred
0029_1482_H95A2_T96-85 (testset)	not.recurred	0.92571	0.07429	not.recurred
0029_1483_H95A2_T96-94 (testset)	not.recurred	0.80998	0.19002	not.recurred
0029_1485_H95A2_T96-136 (testset)	not.recurred	0.93104	0.06896	not.recurred
0029_1486_H95A2_T93-2 (testset)	not.recurred	0.97708	0.02292	not.recurred