StAM Report: Prediction of high risk (predictive) - beta 0.48, 0.52

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

Information on Evaluation

Total number of samples:	37
Training samples:	25 ( 12 from high risk, 13 from low risk )
Test samples:	12 ( 6 from high risk, 6 from low risk )
Focus on class:	high risk
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:	25
Number of classes:	2
Class weights:	'high risk': 0.48 'low risk': 0.52
Class prior:	'high risk':0.48 'low risk':0.52
Shrinkage candidates:	0, 0.038, 0.077, 0.115, 0.154, 0.192, 0.231, 0.269, 0.307, 0.346, 0.384, 0.423, 0.461, 0.5, 0.538, 0.577, 0.615, 0.653, 0.692, 0.73, 0.769, 0.807, 0.846, 0.884, 0.922, 0.961, 0.999, 1.038, 1.076, 1.115

Cross validated performance

Download postscript

Download postscript

	Root.error.rate	Root.performance	Mean.redundancy	Nodes	Genes
0	0.08	1.02026	0.7021	1616	8273
0.038	0.08	0.94242	0.70903	1176	7999
0.077	0.08	0.88784	0.72321	796	7771
0.115	0.08	0.84537	0.7444	556	7109
0.154	0.08	0.79731	0.77834	404	6791
0.192	0.08	0.75494	0.81666	313	6503
0.231	0.08	0.72369	0.85461	250	5691
0.269	0.08	0.70205	0.92316	192	4908
0.307	0.08	0.68524	0.96332	164	4766
0.346	0.08	0.66916	0.9824	150	4474
0.384	0.08	0.64706	1.10829	115	3575
0.423	0.08	0.62098	1.22216	97	3311
0.461	0.08	0.59242	1.24136	93	3199
0.5	0.08	0.57266	1.33856	80	2946
0.538	0.08	0.55382	1.46241	69	2669
0.577	0.08	0.53486	1.53925	64	2531
0.615	0.08	0.51186	1.74695	55	2095
0.653	0.08	0.4942	1.67108	53	1995
0.692	0.08	0.47709	2.05386	40	1595
0.73	0.08	0.45504	2.08658	35	1509
0.769	0.08	0.41994	2.26039	30	1182
0.807	0.08	0.38504	1.90861	30	1182
0.846	0.08	0.35904	4.70191	15	760
0.884	0.08	0.34479	4.78199	15	760
0.922	0.08	0.34745	4.78842	15	760
0.961	0.08	0.35157	4.79823	15	760
0.999	0.08	0.3456	4.51671	15	760
1.038	0.08	0.32857	2.76885	15	760
1.076	0.04	0.32446	5.66119	9	561

Information on Model Fit

Fit for D = 1.0762

Number of classes:	2
Class weights:	'high risk': 0.48 'low risk': 0.52
Class prior:	'high risk':0.48 'low risk':0.52
Chosen shrinkage level:	1.076 (by optimizing the root's error rate )
Number of nodes left	9
Number of accessible genes	561

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:	37 (18 from high risk, 19 from low risk)
Test samples:	12 (6 from high risk, 6 from low risk)
Classes:	high risk, low risk

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	0.00000
GO:0009987	cellular process	0.00000
GO:0007275	development	0.00000
GO:0008371	obsolete biological process	0.00000
GO:0007582	physiological process	1
GO:0050789	regulation of biological process	0.00000
GO:0016032	viral life cycle	0.00000

Performance on training data

• Error rate: 0.08
• Performance: 0.32446
• Redundancy: 5.64765

	Sensitivity	Specificity
high risk	0.91667	0.92308
low risk	0.92308	0.91667

Performance on test data

• Error rate: 0.41667
• Performance: 2.22387
• Redundancy: 3.2679

	Sensitivity	Specificity
high risk	0.5	0.66667
low risk	0.66667	0.5

Predictions

	Class	high risk	low risk	Predictionn
00290952H95A2T01407	low risk	0	1	low risk
00290964H95A2T01439	low risk	0.14714	0.85286	low risk
00290966H95A2T01461	low risk	5e-04	0.9995	low risk
00291004H95A2T01194	high risk	0.18808	0.81192	low risk
00291005H95A2T01047 (testset)	low risk	0	1	low risk
00291046HU95A2-T01-502 (testset)	high risk	0.18718	0.81282	low risk
00291048HU95A2-T01-514 (testset)	low risk	0.39677	0.60323	low risk
00291053HU95A2-T01-618	low risk	0.00312	0.99688	low risk
00291087H95A2-T01-255	high risk	0.99995	5e-05	high risk
00291092H95A2-T01-838	high risk	0.96626	0.03374	high risk
00291126H95A2-T010310	high risk	0.99551	0.00449	high risk
00291127H95A2-T010585 (testset)	high risk	0.96466	0.03534	high risk
00291165HU95A2T01-472	high risk	1	0	high risk
00291187H95A2-T00-0064 (testset)	high risk	0.94226	0.05774	high risk
00291188H95A2-T00-0070 (testset)	high risk	0.36342	0.63658	low risk
00291189H95A2-T00-0109	high risk	0.99896	0.00104	high risk
00291191H95A2-KF67 (testset)	high risk	0.02835	0.97165	low risk
0029_1208_H95A2_KF0076	low risk	0.03446	0.96554	low risk
0029_1209_H95Av2_KF0077	low risk	0	1	low risk
0029_1210_H95A2_KF0079 (testset)	low risk	0.00575	0.99425	low risk
0029_1213_H95A2_KF0110	low risk	0.54066	0.45934	high risk
0029_1221_H95A2_KF0144	low risk	0.01029	0.98971	low risk
0029_1225_H95A2_KF0157	low risk	4e-04	0.9996	low risk
0029_1264_H95A2_KF145	high risk	0.92695	0.07305	high risk
0029_1265_H95A2_KF151	high risk	0.99929	0.00071	high risk
0029_1266_H95A2_KF155	high risk	0.9921	0.0079	high risk
0029_1287_H95A2_KF-184	high risk	0.99446	0.00554	high risk
0029_1289_H95A2_KF-201	high risk	0.99823	0.00177	high risk
0029_1291_H95A2_KF-097	high risk	0.99983	0.00017	high risk
0029_1340_H95A2_KF-069 (testset)	high risk	0.81649	0.18351	high risk
0029_1349_H95A2_KF-113 (testset)	low risk	0.00765	0.99235	low risk
0029_1351_H95A2_KF-117 (testset)	low risk	0.97035	0.02965	high risk
0029_1352_H95A2_KF-120	low risk	6e-05	0.99994	low risk
0029_1375_H95A2_KF-094	low risk	0.01981	0.98019	low risk
0029_1376_H95A2_KF-095 (testset)	low risk	0.93591	0.06409	high risk
0029_1377_H95A2_KF-104	low risk	0.4251	0.5749	low risk
0029_1396_H95A2_KF-105	low risk	0.01262	0.98738	low risk