Output2HTML             Creating HTML file for regressResult or
                        interactionResult class
QC                      sample QC result from Affy Expression Console
Sort                    Sort a regressionResult or an interactionResult
adjustment              Access the multiple comparison adjustment
                        method from the regressResult or
                        interactionResult class
contrastMatrix          Class to Contain the Contrast Matrix that Used
                        for Linear Regression
createExpressionSet     Creating an ExpressionSet
createGSEAFiles         A Wrapper Function to create *.GCT and *.CLS
                        for GSEA analysis
createIndex             Creating an HTML index file
createIngenuityFile     A Wrapper Function to Create Files for
                        Ingenuity Analysis
designMatrix            Class to Contain the Design Matrix that Used
                        for Linear Regression
eSetExample             An ExpressionSet example
exprsExample            a data.frame contains expression data
geneFilter              filter an ExpressionSet using different methods
getAdjP                 access the adjPVal slot from regressResult or
                        interactionResult class
getAnnotation           access the annotation slot from the
                        regressResult or interactionResult slot
getCompare1             Access the Compare1 slot from the
                        contrastMatrix
getCompare2             Access the compare2 slot from the
                        contrastMatrix class
getContrast             Access the contrast matrix from the
                        contrastMatrix class
getCovariates           Accessing the covariates from the designMatrix
                        class
getDesign               Access the design matrix from the designMatrix
                        class
getF                    access the foldChange slot from
                        regressionResult or interactionResult class
getFC                   Access the foldChange slot from the
                        regressResult or interactionResult class
getFCCutoff             Access the significantFCCutoff slot from the
                        regressResult or interactionResult class
getFilterMethod         Access the filterMethod slot from the
                        regressResult or interactionResult class
getID                   access the ID slot from the regressResult or
                        interactionResult class
getIndex                Access the SignificantIndex slot from the
                        regressResult or interactionResult class
getIntIndex             Access the IntIndex slot from the designMatrix
                        class
getInteraction          Access the interaction slot from the
                        contrastMatrix class
getLength               Calculate the Length of interactionResult class
getLevel                Access the level slot from the contrastMatrix
                        class
getNormalizationMethod
                        Access the significantIndex slot from the
                        regressResult or interactionResult class
getP                    Access the pValue slot from regressResult or
                        interactionResult class
getPCutoff              Access the significantPvalueCutoff slot from
                        regressResult or interactionResult class
getTarget               Access the target slots from the designMatrix
                        class
hugene10stCONTROL       hugene10stCONTROL
interactionResult-class
                        Class to Contain the Regression Result Based on
                        An Interaction Model
mogene10stCONTROL       mogene10stCONTROL
output.cls              Create *.CLS file for GSEA analysis
output.gct              Create an *.GCT file for GSEA analysis
output.ing              Create an Ingenuity File for Ingenuity Analysis
pDataExample            a phenoData example
postInteraction         Create an Object of InteractionResult Class for
                        Testing Interaction
preProcess3prime        A wrapper function to normalize the the 3 prime
                        array
preProcessGeneST        Proprocess genechip ST array
qa3prime                Creating Quality Assessment Report for 3 Prime
                        Array
qaGeneST                Creating Quality Assessment Report for Gene ST
                        Array
regress                 Run regression to fit genewise linear model
regressResult-class     Class to Contain the Regression Result
regressionMethod        Access the regressionMethod slot from the
                        regressResult or interactionResult class
selectSigGene           select differentially expressed genes from the
                        regressResult class
selectSigGeneInt        select differentially expressed genes from the
                        interactionResult class
