Entry: Output2HTML
Aliases: Output2HTML
Keywords: 
Description: Creating HTML file for regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/Output2HTML.html

Entry: QC
Aliases: QC
Keywords: datasets
Description: sample QC result from Affy Expression Console
URL: ../../../library/ArrayTools/html/QC.html

Entry: Sort
Aliases: Sort
Keywords: 
Description: Sort a regressionResult or an interactionResult
URL: ../../../library/ArrayTools/html/Sort.html

Entry: adjustment
Aliases: adjustment
Keywords: 
Description: Access the multiple comparison adjustment method from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/adjustment.html

Entry: contrastMatrix
Aliases: contrastMatrix-class contrastMatrix class:contrastMatrix getCompare1,contrastMatrix-method getCompare2,contrastMatrix-method getContrast,contrastMatrix-method getInteraction,contrastMatrix-method getLevel,contrastMatrix-method initialize,contrastMatrix-method show,contrastMatrix-method
Keywords: classes
Description: Class to Contain the Contrast Matrix that Used for Linear Regression
URL: ../../../library/ArrayTools/html/contrastMatrix-class.html

Entry: createExpressionSet
Aliases: createExpressionSet
Keywords: 
Description: Creating an ExpressionSet
URL: ../../../library/ArrayTools/html/createExpressionSet.html

Entry: createGSEAFiles
Aliases: createGSEAFiles
Keywords: 
Description: A Wrapper Function to create *.GCT and *.CLS for GSEA analysis
URL: ../../../library/ArrayTools/html/createGSEAFiles.html

Entry: createIndex
Aliases: createIndex
Keywords: 
Description: Creating an HTML index file
URL: ../../../library/ArrayTools/html/createIndex.html

Entry: createIngenuityFile
Aliases: createIngenuityFile
Keywords: 
Description: A Wrapper Function to Create Files for Ingenuity Analysis
URL: ../../../library/ArrayTools/html/createIngenuityFile.html

Entry: designMatrix
Aliases: designMatrix-class designMatrix class:designMatrix getCovariates,designMatrix-method getDesign,designMatrix-method getIntIndex,designMatrix-method getTarget,designMatrix-method initialize,designMatrix-method show,designMatrix-method
Keywords: classes
Description: Class to Contain the Design Matrix that Used for Linear Regression
URL: ../../../library/ArrayTools/html/designMatrix-class.html

Entry: eSetExample
Aliases: eSetExample
Keywords: datasets
Description: An ExpressionSet example
URL: ../../../library/ArrayTools/html/eSetExample.html

Entry: exprsExample
Aliases: exprsExample
Keywords: datasets
Description: a data.frame contains expression data
URL: ../../../library/ArrayTools/html/exprsExample.html

Entry: geneFilter
Aliases: geneFilter
Keywords: 
Description: filter an ExpressionSet using different methods
URL: ../../../library/ArrayTools/html/geneFilter.html

Entry: getAdjP
Aliases: getAdjP
Keywords: 
Description: access the adjPVal slot from regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getAdjP.html

Entry: getAnnotation
Aliases: getAnnotation
Keywords: 
Description: access the annotation slot from the regressResult or interactionResult slot
URL: ../../../library/ArrayTools/html/getAnnotation.html

Entry: getCompare1
Aliases: getCompare1
Keywords: 
Description: Access the Compare1 slot from the contrastMatrix
URL: ../../../library/ArrayTools/html/getCompare1.html

Entry: getCompare2
Aliases: getCompare2
Keywords: 
Description: Access the compare2 slot from the contrastMatrix class
URL: ../../../library/ArrayTools/html/getCompare2.html

Entry: getContrast
Aliases: getContrast
Keywords: 
Description: Access the contrast matrix from the contrastMatrix class
URL: ../../../library/ArrayTools/html/getContrast.html

Entry: getCovariates
Aliases: getCovariates
Keywords: 
Description: Accessing the covariates from the designMatrix class
URL: ../../../library/ArrayTools/html/getCovariates.html

Entry: getDesign
Aliases: getDesign
Keywords: 
Description: Access the design matrix from the designMatrix class
URL: ../../../library/ArrayTools/html/getDesign.html

Entry: getF
Aliases: getF
Keywords: 
Description: access the foldChange slot from regressionResult or interactionResult class
URL: ../../../library/ArrayTools/html/getF.html

Entry: getFC
Aliases: getFC
Keywords: 
Description: Access the foldChange slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getFC.html

Entry: getFCCutoff
Aliases: getFCCutoff
Keywords: 
Description: Access the significantFCCutoff slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getFCCutoff.html

Entry: getFilterMethod
Aliases: getFilterMethod
Keywords: 
Description: Access the filterMethod slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getFilterMethod.html

Entry: getID
Aliases: getID
Keywords: 
Description: access the ID slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getID.html

Entry: getIndex
Aliases: getIndex
Keywords: 
Description: Access the SignificantIndex slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getIndex.html

Entry: getIntIndex
Aliases: getIntIndex
Keywords: 
Description: Access the IntIndex slot from the designMatrix class
URL: ../../../library/ArrayTools/html/getIntIndex.html

Entry: getInteraction
Aliases: getInteraction
Keywords: 
Description: Access the interaction slot from the contrastMatrix class
URL: ../../../library/ArrayTools/html/getInteraction.html

Entry: getLength
Aliases: getLength
Keywords: 
Description: Calculate the Length of interactionResult class
URL: ../../../library/ArrayTools/html/getLength.html

Entry: getLevel
Aliases: getLevel
Keywords: 
Description: Access the level slot from the contrastMatrix class
URL: ../../../library/ArrayTools/html/getLevel.html

Entry: getNormalizationMethod
Aliases: getNormalizationMethod
Keywords: 
Description: Access the significantIndex slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getNormalizationMethod.html

Entry: getP
Aliases: getP
Keywords: 
Description: Access the pValue slot from regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getP.html

Entry: getPCutoff
Aliases: getPCutoff
Keywords: 
Description: Access the significantPvalueCutoff slot from regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/getPCutoff.html

Entry: getTarget
Aliases: getTarget
Keywords: 
Description: Access the target slots from the designMatrix class
URL: ../../../library/ArrayTools/html/getTarget.html

Entry: hugene10stCONTROL
Aliases: hugene10stCONTROL
Keywords: 
Description: hugene10stCONTROL
URL: ../../../library/ArrayTools/html/hugene10stCONTROL.html

Entry: interactionResult-class
Aliases: interactionResult-class interactionResult class:interactionResult adjustment,interactionResult-method getAdjP,interactionResult-method getAnnotation,interactionResult-method getContrast,interactionResult-method getF,interactionResult-method getFC,interactionResult-method getFCCutoff,interactionResult-method getFileName,interactionResult-method getFilterMethod,interactionResult-method getID,interactionResult-method getIndex,interactionResult-method getLength,interactionResult-method getNormalizationMethod,interactionResult-method getP,interactionResult-method getPCutoff,interactionResult-method Output2HTML,interactionResult-method regressionMethod,interactionResult-method selectSigGene,interactionResult-method show,interactionResult-method Sort,interactionResult-method summary,interactionResult-method
Keywords: classes
Description: Class to Contain the Regression Result Based on An Interaction Model
URL: ../../../library/ArrayTools/html/interactionResult-class.html

Entry: mogene10stCONTROL
Aliases: mogene10stCONTROL
Keywords: 
Description: mogene10stCONTROL
URL: ../../../library/ArrayTools/html/mogene10stCONTROL.html

Entry: output.cls
Aliases: output.cls
Keywords: 
Description: Create *.CLS file for GSEA analysis
URL: ../../../library/ArrayTools/html/output.cls.html

Entry: output.gct
Aliases: output.gct
Keywords: 
Description: Create an *.GCT file for GSEA analysis
URL: ../../../library/ArrayTools/html/output.gct.html

Entry: output.ing
Aliases: output.ing
Keywords: 
Description: Create an Ingenuity File for Ingenuity Analysis
URL: ../../../library/ArrayTools/html/output.ing.html

Entry: pDataExample
Aliases: pDataExample
Keywords: datasets
Description: a phenoData example
URL: ../../../library/ArrayTools/html/pDataExample.html

Entry: postInteraction
Aliases: postInteraction
Keywords: 
Description: Create an Object of InteractionResult Class for Testing Interaction
URL: ../../../library/ArrayTools/html/postInteraction.html

Entry: preProcess3prime
Aliases: preProcess3prime
Keywords: 
Description: A wrapper function to normalize the the 3 prime array
URL: ../../../library/ArrayTools/html/preProcess3prime.html

Entry: preProcessGeneST
Aliases: preProcessGeneST
Keywords: 
Description: Proprocess genechip ST array
URL: ../../../library/ArrayTools/html/preProcessGeneST.html

Entry: qa3prime
Aliases: qa3prime
Keywords: 
Description: Creating Quality Assessment Report for 3 Prime Array
URL: ../../../library/ArrayTools/html/qa3prime.html

Entry: qaGeneST
Aliases: qaGeneST
Keywords: 
Description: Creating Quality Assessment Report for Gene ST Array
URL: ../../../library/ArrayTools/html/qaGeneST.html

Entry: regress
Aliases: regress
Keywords: 
Description: Run regression to fit genewise linear model
URL: ../../../library/ArrayTools/html/regress.html

Entry: regressResult-class
Aliases: regressResult-class regressResult class:regressResult adjustment,regressResult-method getAdjP,regressResult-method getAnnotation,regressResult-method getContrast,regressResult-method getF,regressResult-method getFC,regressResult-method getFCCutoff,regressResult-method getFileName,regressResult-method getFilterMethod,regressResult-method getID,regressResult-method getIndex,regressResult-method getNormalizationMethod,regressResult-method getP,regressResult-method getPCutoff,regressResult-method Output2HTML,regressResult-method regressionMethod,regressResult-method selectSigGene,regressResult-method show,regressResult-method Sort,regressResult-method summary,regressResult-method
Keywords: classes
Description: Class to Contain the Regression Result
URL: ../../../library/ArrayTools/html/regressResult-class.html

Entry: regressionMethod
Aliases: regressionMethod
Keywords: 
Description: Access the regressionMethod slot from the regressResult or interactionResult class
URL: ../../../library/ArrayTools/html/regressionMethod.html

Entry: selectSigGene
Aliases: selectSigGene
Keywords: 
Description: select differentially expressed genes from the regressResult class
URL: ../../../library/ArrayTools/html/selectSigGene.html

Entry: selectSigGeneInt
Aliases: selectSigGeneInt
Keywords: 
Description: select differentially expressed genes from the interactionResult class
URL: ../../../library/ArrayTools/html/selectSigGeneInt.html
