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.

Author
Xiwei Wu, Arthur Li
Date of publication
None
Maintainer
Arthur Li <xueli@coh.org>
License
LGPL (>= 2.0)
Version
1.34.0

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