ExpressionSetWithComputation-class
                        Class "ExpressionSetWithComputation"
a4palette               Utility function that defines a color palette
                        for use in a4
addQuantilesColors      Compute quantiles for plotGeneDE function
boxPlot                 Create a boxplot for a given gene.
combineTwoExpressionSet
                        Combine two ExpressionSet objects
computeLogRatio         Summary statistics for gene expression
createExpressionSet     combine gene expression and phenotype data onto
                        a ExpressionSet object
filterVarInt            Filtering on Intensity and Variance
heatmap.expressionSet   Image plot of an expressionSet
histPvalue              Plot the Distribution of P Values
histpvalueplotter       Workhorse function for the histPvalue function
lassoReg                Multiple regression using the Lasso algorithm
                        as implemented in the glmnet package
limmaReg                Wrapper for the limma function for the
                        comparison of two groups (two factor levels)
limmaTwoLevels          Wrapper for the limma function for the
                        comparison of two groups (two factor levels)
logReg                  Logistic regression for predicting the
                        probability to belong to a certain class in
                        binary classification problems
nlcvTT                  Data to Demonstrate nlcv and Co Functions
oaColors                Pick One or More OA Colors
oaPalette               Generate a Palette of OA Colors
plot1gene               Create a Profile Plot for a given Gene
plotComb2Samples        Plots the correlation in gene expression
                        between two samples
plotCombMultSamples     Plots the correlation in gene expression
                        between more than 2 samples
plotCombination2genes   Plot a Combination of Two Genes
plotLogRatio            Plot a summary gene expression graph
probabilitiesPlot       Function to plot the probabilities to belong to
                        a certain class in binary classification
                        problems.
probe2gene              Translate Affymetrix probeset IDs into gene
                        symbols
profilesPlot            Plot expression profiles of multiple genes or
                        probesets Plot expression profiles of multiple
                        genes or probesets. Each line depicts a gene,
                        and the color legend can be used to identify
                        the gene.
propDEgenes             Generic function to compute the proportion of
                        differentially expressed genes that are present
propDEgenes-methods     Generic function to compute the proportion of
                        differentially expressed genes that are present
propdegenescalculation
                        Estimation of proportion of differentially
                        expressed genes
replicates              computes replicates across a vector
spectralMap             Generic function to draw a spectral map,
                        according to JnJ Standards
spectralMap-methods     Methods for Function spectralMap according to
                        JnJ Standards
tTest                   Use t Test to Compare Two Groups
topTable,limma-method   Methods for topTable
volcanoPlot             Draw a Volcano Plot
volcanoPlot-methods     Draw a Volcano Plot
volcanoplotter          Workhorse function for the different
                        volcanoPlot methods
