| edge-package | Extraction of Differential Gene Expression |
| apply_jackstraw | Non-Parametric Jackstraw for Principal Component Analysis (PCA) |
| apply_jackstraw-method | Non-Parametric Jackstraw for Principal Component Analysis (PCA) |
| apply_qvalue | Estimate the q-values for a given set of p-values |
| apply_qvalue-method | Estimate the q-values for a given set of p-values |
| apply_snm | Supervised normalization of data in edge |
| apply_snm-method | Supervised normalization of data in edge |
| apply_sva | Estimate surrogate variables |
| apply_sva-method | Estimate surrogate variables |
| betaCoef | Regression coefficients from full model fit |
| betaCoef-method | Regression coefficients from full model fit |
| build_models | Generate a deSet object with full and null models |
| build_study | Formulates the experimental models |
| deFit-class | The differential expression class for the model fits |
| deSet | Create a deSet object from an ExpressionSet |
| deSet-class | The differential expression class (deSet) |
| deSet-method | Create a deSet object from an ExpressionSet |
| edge | Extraction of Differential Gene Expression |
| endotoxin | Gene expression dataset from Calvano et al. (2005) Nature |
| fitFull | Fitted data from the full model |
| fitFull-method | Fitted data from the full model |
| fitNull | Fitted data from the null model |
| fitNull-method | Fitted data from the null model |
| fit_models | Linear regression of the null and full models |
| fit_models-method | Linear regression of the null and full models |
| fullMatrix | Matrix representation of full model |
| fullMatrix-method | Matrix representation of full model |
| fullMatrix<- | Matrix representation of full model |
| fullMatrix<--method | Matrix representation of full model |
| fullModel | Full model equation |
| fullModel-method | Full model equation |
| fullModel<- | Full model equation |
| fullModel<--method | Full model equation |
| gibson | Gene expression dataset from Idaghdour et al. (2008) |
| individual | Individuals sampled in experiment |
| individual-method | Individuals sampled in experiment |
| individual<- | Individuals sampled in experiment |
| individual<--method | Individuals sampled in experiment |
| kidney | Gene expression dataset from Rodwell et al. (2004) |
| kl_clust | Modular optimal discovery procedure (mODP) |
| kl_clust-method | Modular optimal discovery procedure (mODP) |
| lrt | Performs F-test (likelihood ratio test using Normal likelihood) |
| lrt-method | Performs F-test (likelihood ratio test using Normal likelihood) |
| nullMatrix | Matrix representation of null model |
| nullMatrix-method | Matrix representation of null model |
| nullMatrix<- | Matrix representation of null model |
| nullMatrix<--method | Matrix representation of null model |
| nullModel | Null model equation from deSet object |
| nullModel-method | Null model equation from deSet object |
| nullModel<- | Null model equation from deSet object |
| nullModel<--method | Null model equation from deSet object |
| odp | The optimal discovery procedure |
| odp-method | The optimal discovery procedure |
| qvalueObj | Access/set qvalue slot |
| qvalueObj-method | Access/set qvalue slot |
| qvalueObj<- | Access/set qvalue slot |
| qvalueObj<--method | Access/set qvalue slot |
| resFull | Residuals of full model fit |
| resFull-method | Residuals of full model fit |
| resNull | Residuals of null model fit |
| resNull-method | Residuals of null model fit |
| show | Show function for deFit and deSet |
| show-method | Show function for deFit and deSet |
| sType | Statistic type used in analysis |
| sType-method | Statistic type used in analysis |
| summary | Summary of deFit and deSet |
| summary-method | Summary of deFit and deSet |