Ritchie Lab environment: RHEL6 with RCC storage Loading required package: Matrix Loading required package: methods Loading required package: lattice Loaded glmnet 1.9-3 Loading required package: MASS Loading required package: nnet Loading required package: car Loading required package: arm Loading required package: lme4 Attaching package: ‘lme4’ The following object(s) are masked from ‘package:stats’: AIC, BIC Loading required package: R2WinBUGS Loading required package: coda Attaching package: ‘coda’ The following object(s) are masked from ‘package:lme4’: HPDinterval Loading required package: boot Attaching package: ‘boot’ The following object(s) are masked from ‘package:car’: logit The following object(s) are masked from ‘package:lattice’: melanoma Loading required package: abind Loading required package: foreign arm (Version 1.6-06.01, built: 2013-5-9) Working directory is /gpfs/group1/m/mdr23/projects/biobin/CF_dbGaP/biobin/covfiles Attaching package: ‘arm’ The following object(s) are masked from ‘package:boot’: logit The following object(s) are masked from ‘package:coda’: traceplot The following object(s) are masked from ‘package:car’: logit mi (Version 0.09-18, built: 2012-09-05) Warning message: package ‘abind’ was built under R version 2.15.2 Loading required package: cluster Loading required package: foreach Loading required package: plyr Loading required package: reshape2 Loading required package: iterators Loading required package: parallel Loading required package: class Loading required package: pROC Type 'citation("pROC")' for a citation. Attaching package: ‘pROC’ The following object(s) are masked from ‘package:glmnet’: auc The following object(s) are masked from ‘package:stats’: cov, smooth, var [1] 1 [1] 2 [1] 3 ------------------------------------------------------- Cross-Validation: 1 ------------------------------------------------------- Tuned values: .alpha .lambda 152 0.6 0.2 Non-zero coefficients: [1] 3.700993 Measured statistics with best model: Confusion Matrix and Statistics Reference Prediction 0 1 0 25 3 1 5 23 Accuracy : 0.8571 95% CI : (0.7378, 0.9362) No Information Rate : 0.5357 P-Value [Acc > NIR] : 3.657e-07 Kappa : 0.7143 Mcnemar's Test P-Value : 0.7237 Sensitivity : 0.8333 Specificity : 0.8846 Pos Pred Value : 0.8929 Neg Pred Value : 0.8214 Prevalence : 0.5357 Detection Rate : 0.4464 Detection Prevalence : 0.5000 'Positive' Class : 0 ------------------------------------------------------- Cross-Validation: 2 ------------------------------------------------------- Tuned values: .alpha .lambda 241 0.9 0.1 Non-zero coefficients: (Intercept) cov.PC8 GLI4 PRMT3 LMO7_NS CLYBL 6.17951783 0.69394086 0.21356508 0.03783761 0.40442343 0.30446194 URI1 ATP5O VPREB1 0.35866321 0.27781488 0.04144064 Measured statistics with best model: Confusion Matrix and Statistics Reference Prediction 0 1 0 25 7 1 8 31 Accuracy : 0.7887 95% CI : (0.6756, 0.8767) No Information Rate : 0.5352 P-Value [Acc > NIR] : 8.284e-06 Kappa : 0.5745 Mcnemar's Test P-Value : 1 Sensitivity : 0.7576 Specificity : 0.8158 Pos Pred Value : 0.7812 Neg Pred Value : 0.7949 Prevalence : 0.4648 Detection Rate : 0.3521 Detection Prevalence : 0.4507 'Positive' Class : 0 ------------------------------------------------------- Cross-Validation: 3 ------------------------------------------------------- Tuned values: .alpha .lambda 123 0.5 0.3 Non-zero coefficients: [1] 3.064058 Measured statistics with best model: Confusion Matrix and Statistics Reference Prediction 0 1 0 25 2 1 6 21 Accuracy : 0.8519 95% CI : (0.7288, 0.9338) No Information Rate : 0.5741 P-Value [Acc > NIR] : 1.182e-05 Kappa : 0.7037 Mcnemar's Test P-Value : 0.2888 Sensitivity : 0.8065 Specificity : 0.9130 Pos Pred Value : 0.9259 Neg Pred Value : 0.7778 Prevalence : 0.5741 Detection Rate : 0.4630 Detection Prevalence : 0.5000 'Positive' Class : 0 Ritchie Lab environment: RHEL6 with RCC storage