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