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.

AuthorXiwei Wu, Arthur Li
Date of publicationNone
MaintainerArthur Li <xueli@coh.org>
LicenseLGPL (>= 2.0)
Version1.34.0

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

output.ing: 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

Files in this package

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

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