ArrayTools: geneChip Analysis Package

This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Install the latest version of this package by entering the following in R:
AuthorXiwei Wu, Arthur Li
Bioconductor views Annotation DifferentialExpression Microarray OneChannel Preprocessing QualityControl ReportWriting StatisticalMethod Visualization
Date of publicationNone
MaintainerArthur Li <>
LicenseLGPL (>= 2.0)

View on Bioconductor

Man pages

adjustment: Access the multiple comparison adjustment method from the...

contrastMatrix-class: Class to Contain the Contrast Matrix that Used for Linear...

createExpressionSet: Creating an ExpressionSet

createGSEAFiles: A Wrapper Function to create *.GCT and *.CLS for GSEA...

createIndex: Creating an HTML index file

createIngenuityFile: A Wrapper Function to Create Files for Ingenuity Analysis

designMatrix-class: Class to Contain the Design Matrix that Used for Linear...

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...

getAnnotation: access the annotation slot from the regressResult or...

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...

getFC: Access the foldChange slot from the regressResult or...

getFCCutoff: Access the significantFCCutoff slot from the regressResult or...

getFilterMethod: Access the filterMethod slot from the regressResult or...

getID: access the ID slot from the regressResult or...

getIndex: Access the SignificantIndex slot from the regressResult or...

getInteraction: Access the interaction slot from the contrastMatrix class

getIntIndex: Access the IntIndex slot from the designMatrix 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...

getP: Access the pValue slot from regressResult or...

getPCutoff: Access the significantPvalueCutoff slot from regressResult or...

getTarget: Access the target slots from the designMatrix class

hugene10stCONTROL: hugene10stCONTROL

interactionResult-class: Class to Contain the Regression Result Based on An...

mogene10stCONTROL: mogene10stCONTROL

Output2HTML: Creating HTML file for regressResult or interactionResult...

output.cls: Create *.CLS file for GSEA analysis

output.gct: Create an *.GCT file for GSEA analysis Create an Ingenuity File for Ingenuity Analysis

pDataExample: a phenoData example

postInteraction: Create an Object of InteractionResult Class for Testing...

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

QC: sample QC result from Affy Expression Console

regress: Run regression to fit genewise linear model

regressionMethod: Access the regressionMethod slot from the regressResult or...

regressResult-class: Class to Contain the Regression Result

selectSigGene: select differentially expressed genes from the regressResult...

selectSigGeneInt: select differentially expressed genes from the...

Sort: Sort a regressionResult or an interactionResult


adjustment Man page
adjustment,interactionResult-method Man page
adjustment,regressResult-method Man page
class:contrastMatrix Man page
class:designMatrix Man page
class:interactionResult Man page
class:regressResult Man page
contrastMatrix Man page
contrastMatrix-class Man page
createExpressionSet Man page
createGSEAFiles Man page
createIndex Man page
createIngenuityFile Man page
designMatrix Man page
designMatrix-class Man page
eSetExample Man page
exprsExample Man page
geneFilter Man page
getAdjP Man page
getAdjP,interactionResult-method Man page
getAdjP,regressResult-method Man page
getAnnotation Man page
getAnnotation,interactionResult-method Man page
getAnnotation,regressResult-method Man page
getCompare1 Man page
getCompare1,contrastMatrix-method Man page
getCompare2 Man page
getCompare2,contrastMatrix-method Man page
getContrast Man page
getContrast,contrastMatrix-method Man page
getContrast,interactionResult-method Man page
getContrast,regressResult-method Man page
getCovariates Man page
getCovariates,designMatrix-method Man page
getDesign Man page
getDesign,designMatrix-method Man page
getF Man page
getFC Man page
getFCCutoff Man page
getFCCutoff,interactionResult-method Man page
getFCCutoff,regressResult-method Man page
getFC,interactionResult-method Man page
getFC,regressResult-method Man page
getFileName,interactionResult-method Man page
getFileName,regressResult-method Man page
getFilterMethod Man page
getFilterMethod,interactionResult-method Man page
getFilterMethod,regressResult-method Man page
getF,interactionResult-method Man page
getF,regressResult-method Man page
getID Man page
getID,interactionResult-method Man page
getID,regressResult-method Man page
getIndex Man page
getIndex,interactionResult-method Man page
getIndex,regressResult-method Man page
getInteraction Man page
getInteraction,contrastMatrix-method Man page
getIntIndex Man page
getIntIndex,designMatrix-method Man page
getLength Man page
getLength,interactionResult-method Man page
getLevel Man page
getLevel,contrastMatrix-method Man page
getNormalizationMethod Man page
getNormalizationMethod,interactionResult-method Man page
getNormalizationMethod,regressResult-method Man page
getP Man page
getPCutoff Man page
getPCutoff,interactionResult-method Man page
getPCutoff,regressResult-method Man page
getP,interactionResult-method Man page
getP,regressResult-method Man page
getTarget Man page
getTarget,designMatrix-method Man page
hugene10stCONTROL Man page
initialize,contrastMatrix-method Man page
initialize,designMatrix-method Man page
interactionResult Man page
interactionResult-class Man page
mogene10stCONTROL Man page
Output2HTML Man page
Output2HTML,interactionResult-method Man page
Output2HTML,regressResult-method Man page
output.cls Man page
output.gct Man page Man page
pDataExample Man page
postInteraction Man page
preProcess3prime Man page
preProcessGeneST Man page
qa3prime Man page
qaGeneST Man page
QC Man page
regress Man page
regressionMethod Man page
regressionMethod,interactionResult-method Man page
regressionMethod,regressResult-method Man page
regressResult Man page
regressResult-class Man page
selectSigGene Man page
selectSigGeneInt Man page
selectSigGene,interactionResult-method Man page
selectSigGene,regressResult-method Man page
show,contrastMatrix-method Man page
show,designMatrix-method Man page
show,interactionResult-method Man page
show,regressResult-method Man page
Sort Man page
Sort,interactionResult-method Man page
Sort,regressResult-method Man page
summary,interactionResult-method Man page
summary,regressResult-method Man page


R/Generic.R R/contrastMatrix-class.R R/createExpressionSet.R R/createGSEAFiles.R R/createIndex.R R/createIngenuityFile.R R/designMatrix-class.R R/geneFilter.R R/intensityPlot.R R/interactionResult-class.R R/output.cls.R R/output.gct.R R/ R/plotCluster.R R/postInteraction.R R/preProcess3prime.R R/preProcessGeneST.R R/qa3prime.R R/qaGeneST.R R/regress.R R/regressResult-class.R R/selectSigGene.R R/selectSigGeneInt.R
man/Output2HTML.Rd man/QC.Rd man/Sort.Rd man/adjustment.Rd man/contrastMatrix-class.Rd man/createExpressionSet.Rd man/createGSEAFiles.Rd man/createIndex.Rd man/createIngenuityFile.Rd man/designMatrix-class.Rd man/eSetExample.Rd man/exprsExample.Rd man/geneFilter.Rd man/getAdjP.Rd man/getAnnotation.Rd man/getCompare1.Rd man/getCompare2.Rd man/getContrast.Rd man/getCovariates.Rd man/getDesign.Rd man/getF.Rd man/getFC.Rd man/getFCCutoff.Rd man/getFilterMethod.Rd man/getID.Rd man/getIndex.Rd man/getIntIndex.Rd man/getInteraction.Rd man/getLength.Rd man/getLevel.Rd man/getNormalizationMethod.Rd man/getP.Rd man/getPCutoff.Rd man/getTarget.Rd man/hugene10stCONTROL.Rd man/interactionResult-class.Rd man/mogene10stCONTROL.Rd man/output.cls.Rd man/output.gct.Rd man/ man/pDataExample.Rd man/postInteraction.Rd man/preProcess3prime.Rd man/preProcessGeneST.Rd man/qa3prime.Rd man/qaGeneST.Rd man/regress.Rd man/regressResult-class.Rd man/regressionMethod.Rd man/selectSigGene.Rd man/selectSigGeneInt.Rd

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