DGEExact-class          differential expression of Digital Gene
                        Expression data - class
DGEGLM-class            Digital Gene Expression Generalized Linear
                        Model results - class
DGELRT-class            Digital Gene Expression Likelihood Ratio Test
                        data and results - class
DGEList                 DGEList Constructor
DGEList-class           Digital Gene Expression data - class
Tu102                   Raw Data for Several SAGE Libraries from the
                        Zhang 1997 Science Paper.
approx.expected.info    Approximate Expected Information (Fisher
                        Information)
betaApproxNBTest        An Approximate Exact Test for Differences
                        between Two Negative Binomial Groups
binMeanVar              Explore the mean-variance relationship for DGE
                        data
calcNormFactors         Calculates Normalization Factors for a Matrix
                        of Count Data
commonCondLogLikDerDelta
                        Conditional Log-Likelihoods in Terms of Delta
condLogLikDerDelta      Conditional Log-Likelihood in Terms of Delta
condLogLikDerSize       Log-Likelihood of the Common Dispersion for a
                        Single Equalized Group
decideTestsDGE          Multiple Testing Across Genes and Contrasts
dglmStdResid            Visualize the mean-variance relationship in DGE
                        data using standardized residuals
dim.DGEList             Retrieve the Dimensions of a DGEList, DGEExact,
                        DGEGLM, DGELRT or TopTags Object
dimnames.DGEList        Retrieve the Dimension Names of a DGEList
                        Object
edgeR-package           Empirical analysis of digital gene expression
                        data in R
equalizeLibSizes        Quantile Adjustment to Equalize Library Sizes
                        for a Fixed Value of the Dispersion Parameter
estimateCRDisp          Estimate the dispersion parameter for a
                        negative binomial model using Cox-Reid
                        approximate conditional inference
estimateCommonDisp      Estimates the Negative Binomial Common
                        Dispersion by Maximizing the Negative Binomial
                        Conditional Common Likelihood
estimatePs              Estimate Expression Levels
estimateSmoothing       Estimate the Prior Weight
estimateTagwiseDisp     Maximizes the Negative Binomial Weighted
                        Conditional Likelihood
exactTest               An Exact Test for Differences between Two
                        Negative Binomial Groups
getCounts               Extract Table of Counts from DGEList Object
glmFit                  Fit negative binomial generalized linear model
                        for each transcript
goodTuring              Good-Turing Frequency Estimation
logLikDerP              Log-Likelihood for Proportion
maPlot                  Plots Log-Fold Change versus Log-Concentration
                        (or, M versus A) for Count Data
mglm                    Fit a negative binomial generalized linear
                        model to multiple response vectors
plotMDS.dge             Multidimensional scaling plot of SAGE data
plotSmear               Plots log-Fold Change versus log-Concentration
                        (or, M versus A) for Count Data
q2qnbinom               Quantile to Quantile Mapping between
                        Negative-Binomial Distributions
readDGE                 Read and Merge a Set of Files Containing DGE
                        Data
splitIntoGroups         Split the Counts or Pseudocounts from a DGEList
                        Object According To Group
subsetting              Subset DGEList and DGEExact Objects
topTags                 Table of the Top Differentially Expressed Tags
weightedComLik          Weighted Common Log-Likelihood
weightedCondLogLikDerDelta
                        Weighted Conditional Log-Likelihood in Terms of
                        Delta
