# Extraction of Differential Gene Expression

## Documentation for package ‘edge’ version 2.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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