AffyExpress: Affymetrix Quality Assessment and Analysis Tool
Version 1.42.0

The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

AuthorXiwei Wu <xwu@coh.org>, Xuejun Arthur Li <xueli@coh.org>
Bioconductor views Annotation DifferentialExpression Microarray OneChannel Preprocessing QualityControl ReportWriting Visualization
Date of publicationNone
MaintainerXuejun Arthur Li <xueli@coh.org>
LicenseLGPL
Version1.42.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AffyExpress")

Popular man pages

AffyInteraction: Analyze interaction effect and produce output
AffyQA: Microarray quality control and assessment
AffyRegress: Select differentially expressed genes, and output the result...
Filter: filter an 'ExpressionSet' using different methods
make.contrast: Create a contrast matrix
regress: Run regression to fit genewise linear model
select.sig.gene: select differentially expressed genes based on p value and/or...
See all...

All man pages Function index File listing

Man pages

AffyInteraction: Analyze interaction effect and produce output
AffyQA: Microarray quality control and assessment
AffyRegress: Select differentially expressed genes, and output the result...
Filter: filter an 'ExpressionSet' using different methods
import.data: Importing Affy Cel File
interaction.result2html: output differentially expressed genes for the interaction...
make.contrast: Create a contrast matrix
make.design: Create a Design Matrix
post.interaction: Create a list of tables for the result based on the main...
pre.process: Data Preprocessing
regress: Run regression to fit genewise linear model
result2html: output differentially expressed genes to a HTML file
select.sig.gene: select differentially expressed genes based on p value and/or...
testData: AffyBatch instance testData

Functions

Files

DESCRIPTION
NAMESPACE
R
R/AffyInteraction.R
R/AffyQA.R
R/AffyRegress.R
R/Filter.R
R/SortMat.R
R/cal.eq.R
R/f.test.R
R/find.col.index.R
R/get.f.R
R/import.data.R
R/interaction.result2html.R
R/make.contrast.R
R/make.design.R
R/make.formula.R
R/permute.1.R
R/post.interaction.R
R/pre.process.R
R/regress.R
R/result2html.R
R/select.sig.gene.R
build
build/vignette.rds
data
data/testData.rda
inst
inst/doc
inst/doc/AffyExpress.R
inst/doc/AffyExpress.Rnw
inst/doc/AffyExpress.pdf
man
man/AffyInteraction.Rd
man/AffyQA.Rd
man/AffyRegress.Rd
man/Filter.Rd
man/import.data.Rd
man/interaction.result2html.Rd
man/make.contrast.Rd
man/make.design.Rd
man/post.interaction.Rd
man/pre.process.Rd
man/regress.Rd
man/result2html.Rd
man/select.sig.gene.Rd
man/testData.Rd
vignettes
vignettes/AffyExpress.Rnw
AffyExpress documentation built on May 20, 2017, 9:25 p.m.

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