AffyExpress: Affymetrix Quality Assessment and Analysis Tool

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.

Author
Xiwei Wu <xwu@coh.org>, Xuejun Arthur Li <xueli@coh.org>
Date of publication
None
Maintainer
Xuejun Arthur Li <xueli@coh.org>
License
LGPL
Version
1.40.0

View on Bioconductor

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

Files in this package

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