affy: Methods for Affymetrix Oligonucleotide Arrays
Version 1.54.0

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Browse man pages Browse package API and functions Browse package files

AuthorRafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang
Bioconductor views Microarray OneChannel Preprocessing
Date of publicationNone
MaintainerRafael A. Irizarry <rafa@jhu.edu>
LicenseLGPL (>= 2.0)
Version1.54.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("affy")

Man pages

AffyBatch-class: Class AffyBatch
affy-deprecated: Deprecated functions in package 'affy'
affy-options: Options for the affy package
AffyRNAdeg: Function to assess RNA degradation in Affymetrix GeneChip...
affy.scalevalue.exprSet: Scale normalization for expreSets
barplot.ProbeSet: show a ProbeSet as barplots
bg.adjust: Background adjustment (internal function)
bgc: Background Correction
cdfenv.example: Example cdfenv
cdfFromBioC: Functions to obtain CDF files
cleancdfname: Clean Affymetrix's CDF name
debug.affy123: Debugging Flag
expresso: From raw probe intensities to expression values
expressoWidget: A widget for users to pick correction methods
fit.li.wong: Fit Li and Wong Model to a Probe Set
generateExprSet-methods: generate a set of expression values
generateExprVal.method.avgdiff: Generate an expression value from the probes informations
generateExprVal.method.playerout: Generate an expression value from the probes informations
generateExprVal-methods: Compute a summary expression value from the probes...
hlog: Hybrid Log
justrma: Read CEL files into an ExpressionSet
list.celfiles: List the Cel Files in a Directory/Folder
maffy.subset: Select Subset
MAplot: Relative M vs. A plots
mas5: MAS 5.0 expression measure
mas5calls: MAS 5.0 Absolute Detection
merge.AffyBatch: merge two AffyBatch objects
mva.pairs: M vs. A Matrix
normalize.constant: Scale probe intensities
normalize.contrast: Normalize intensities using the contrasts method
normalize.invariantset: Invariant Set normalization
normalize.loess: Scale microarray data
normalize-methods: Normalize Affymetrix Probe Level Data - methods
normalize.qspline: Normalize arrays
normalize.quantiles: Quantile Normalization
normalize.quantiles.robust: Robust Quantile Normalization
pairs.AffyBatch: plot intensities using 'pairs'
plot.density: Plot Densities
plotLocation: Plot a location on a cel image
plot.ProbeSet: plot a probe set
pmcorrect: PM Correction
ppsetApply: Apply a function over the ProbeSets in an AffyBatch
probeMatch-methods: Methods for accessing perfect matches and mismatches
probeNames-methods: Methods for accessing the Probe Names
ProbeSet-class: Class ProbeSet
ProgressBarText-class: Class "ProgressBarText"
read.affybatch: Read CEL files into an AffyBatch
read.probematrix: Read CEL file data into PM or MM matrices
rma: Robust Multi-Array Average expression measure
setAffyOptions: ~~function to set options ~~
SpikeIn: SpikeIn Experiment Data: ProbeSet Example
summary: Probe Set Summarizing Functions
tukey.biweight: One-step Tukey's biweight
whatcdf: Find which CDF corresponds
xy2indices: Functions to convert indices to x/y (and reverse)

Functions

$.AffyBatch Man page
.setAffyOptions Man page
AffyBatch Man page
AffyBatch,ANY Man page
AffyBatch-class Man page
AffyRNAdeg Man page
AllButCelsForReadAffy Man page Source code
MAplot Man page
MAplot,AffyBatch-method Man page
Mbox Man page
Mbox,AffyBatch-method Man page
ProbeSet-class Man page
ProgressBarText-class Man page
ReadAffy Man page Source code
SpikeIn Man page
[,AffyBatch-method Man page
[<-,AffyBatch-method Man page
[[,AffyBatch-method Man page
affy-options Man page
affy.scalevalue.exprSet Man page Source code
avdiff Man page Source code Source code
barplot,ProbeSet-method Man page
barplot.ProbeSet Man page Source code
bg.adjust Man page Source code
bg.correct Man page
bg.correct,AffyBatch,character-method Man page
bg.correct.mas Man page Source code
bg.correct.none Man page Source code
bg.correct.rma Man page Source code
bg.correct.subtractmm Man page
bg.parameters Man page Source code
bgcorrect Man page
bgcorrect.methods Man page Source code
boxplot,AffyBatch-method Man page
cdfFromBioC Man page Source code
cdfFromEnvironment Man page Source code
cdfFromLibPath Man page Source code
cdfName Man page
cdfName,AffyBatch-method Man page Man page
cdfenv.example Man page
checkValidFilenames Man page Source code
cleancdfname Man page Source code
close,ProgressBarText-method Man page
col,AffyBatch-method Man page
colnames,ProbeSet-method Man page
computeExprSet Man page
computeExprSet,AffyBatch,character,character-method Man page
concentrations Man page
debug.affy123 Man page
dim,AffyBatch-method Man page
express.summary.stat Man page
express.summary.stat,ProbeSet,character,character-method Man page
express.summary.stat-methods Man page
express.summary.stat.methods Man page Source code
expresso Man page Source code
expressoWidget Man page Source code
exprs,AffyBatch-method Man page
exprs<-,AffyBatch,ANY-method Man page
featureNames,AffyBatch-method Man page
featureNames<-,AffyBatch-method Man page
fit.li.wong Man page Source code
geneNames Man page
geneNames,AffyBatch-method Man page
geneNames<- Man page
geneNames<-,AffyBatch,ANY-method Man page
generateExprSet-methods Man page
generateExprSet.methods Man page Source code
generateExprVal.method.avgdiff Man page Source code
generateExprVal.method.liwong Man page Source code
generateExprVal.method.mas Man page Source code
generateExprVal.method.medianpolish Man page Source code
generateExprVal.method.playerout Man page Source code
getCdfInfo Man page Source code
getCdfInfo,AffyBatch-method Man page
hist,AffyBatch-method Man page
hlog Man page Source code
image Man page
image,AffyBatch-method Man page
indexProbes Man page
indexProbes,AffyBatch,character-method Man page
indexProbes,AffyBatch,missing-method Man page
indexProbes,AffyBatch-method Man page
indices2xy Man page Source code
initialize,AffyBatch-method Man page
initialize,ProgressBarText-method Man page
intensity Man page
intensity,AffyBatch-method Man page
intensity<- Man page
intensity<-,AffyBatch-method Man page
just.rma Man page Source code
justRMA Man page Source code
length,AffyBatch-method Man page
li.wong Man page Source code
list.celfiles Man page Source code
loess.normalize Man page Source code
ma.plot Man page Source code
maffy.normalize Man page Source code
maffy.subset Man page Source code
mapCdfName Man page
mas5 Man page Source code
mas5.detection Man page Source code
mas5calls Man page
mas5calls,AffyBatch-method Man page
mas5calls,ProbeSet-method Man page
mas5calls.AffyBatch Man page Source code
mas5calls.ProbeSet Man page Source code
matdensity Man page
medianpolish Man page Source code
merge.AffyBatch Man page Source code
mm Man page
mm,AffyBatch-method Man page
mm,ProbeSet-method Man page
mm<- Man page
mm<-,AffyBatch,ANY-method Man page
mm<-,ProbeSet,matrix-method Man page
mmindex Man page
mmindex,AffyBatch-method Man page
multiloess Man page Source code
mva.pairs Man page Source code
nitBackgroundCorrect Source code
nitExpression Source code
nitNormalize Source code
nitPmCorrect Source code
normalize,AffyBatch-method Man page
normalize.AffyBatch Man page
normalize.AffyBatch.constant Man page Source code
normalize.AffyBatch.contrasts Man page Source code
normalize.AffyBatch.invariantset Man page Source code
normalize.AffyBatch.loess Man page Source code
normalize.AffyBatch.methods Man page Man page Source code
normalize.AffyBatch.qspline Man page Source code
normalize.AffyBatch.quantiles Man page Source code
normalize.AffyBatch.quantiles.robust Man page Source code
normalize.constant Man page Source code
normalize.contrasts Man page
normalize.invariantset Man page Source code
normalize.loess Man page Source code
normalize.methods Man page
normalize.methods,AffyBatch-method Man page
normalize.qspline Man page Source code
onLoad Source code
open,ProgressBarText-method Man page
pairs.AffyBatch Man page Source code
playerout.costfunction Man page Source code
plot.ProbeSet Man page Source code
plotAffyRNAdeg Man page
plotDensity Man page Source code
plotDensity.AffyBatch Man page Source code
plotLocation Man page Source code
pm Man page
pm,AffyBatch-method Man page
pm,ProbeSet-method Man page
pm<- Man page
pm<-,AffyBatch,ANY-method Man page
pm<-,ProbeSet,matrix-method Man page
pmcorrect Man page
pmcorrect.mas Man page Source code
pmcorrect.methods Man page Source code
pmcorrect.pmonly Man page Source code
pmcorrect.subtractmm Man page Source code
pmindex Man page
pmindex,AffyBatch-method Man page
ppset.ttest Man page Source code
ppsetApply Man page Source code
probeMatch Man page
probeMatch-methods Man page
probeName Man page
probeName<- Man page
probeNames Man page
probeNames,AffyBatch-method Man page
probeNames-methods Man page
probeNames<- Man page
probes Man page
probes,AffyBatch-method Man page
probeset Man page
probeset,AffyBatch-method Man page
qspline-normalize Man page
read.affybatch Man page Source code
read.probematrix Man page Source code
rma Man page Source code
row,AffyBatch-method Man page
sampleNames,ProbeSet-method Man page
se.exprs,AffyBatch-method Man page
se.exprs<-,AffyBatch-method Man page
setAffyOptions Source code
show,AffyBatch-method Man page
show,ProbeSet-method Man page
simplemultiLoess Man page Source code
summary Man page
summaryAffyRNAdeg Man page
tukey.biweight Man page Source code
tukeybiweight Man page Source code Source code
upDate.bgcorrect.methods Man page Source code
upDate.express.summary.stat.methods Man page Source code
upDate.generateExprSet.methods Man page Source code
upDate.normalize.AffyBatch.methods Man page Source code
upDate.pmcorrect.methods Man page Source code
updateMe Man page
updateMe,ProgressBarText-method Man page
updateObject,AffyBatch-method Man page
whatcdf Man page Source code
xy2indices Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AffyBatch.R
R/AffyRNAdeg.R
R/ProbeSet.R
R/ProgressBarText.R
R/avdiff.R
R/barplot.ProbeSet.R
R/bg.Affy.chipwide.R
R/bg.R
R/expresso.R
R/expressoWidget.R
R/fit.li.wong.R
R/generateExprVal.method.avgdiff.R
R/generateExprVal.method.liwong.R
R/generateExprVal.method.mas.R
R/generateExprVal.method.medianpolish.R
R/generateExprVal.method.playerout.R
R/getCDFenv.R
R/hlog.R
R/justrma.R
R/loess.normalize.R
R/maffy.R
R/mas5.R
R/merge.AffyBatch.R
R/mva.pairs.R
R/normalize.constant.R
R/normalize.contrasts.R
R/normalize.invariantset.R
R/normalize.loess.R
R/normalize.qspline.R
R/normalize.quantiles.R
R/pairs.AffyBatch.R
R/plot.ProbeSet.R
R/plot.density.R
R/plotLocation.R
R/pmcorrect.mas.R
R/ppset.ttest.R
R/ppsetApply.R
R/read.affybatch.R
R/rma.R
R/summary.R
R/tukey.biweight.R
R/whatcdf.R
R/xy2indices.R
R/zzz.R
aclocal.m4
build
build/vignette.rds
changelog
cleanup
configure
configure.in
data
data/SpikeIn.rda
data/cdfenv.example.rda
data/mapCdfName.rda
demo
demo/00Index
demo/affy.tour.R
inst
inst/CITATION
inst/doc
inst/doc/affy.R
inst/doc/affy.Rnw
inst/doc/affy.pdf
inst/doc/builtinMethods.R
inst/doc/builtinMethods.Rnw
inst/doc/builtinMethods.pdf
inst/doc/customMethods.R
inst/doc/customMethods.Rnw
inst/doc/customMethods.pdf
inst/doc/vim.R
inst/doc/vim.Rnw
inst/doc/vim.pdf
inst/tests
inst/tests/affybatch.R
inst/tests/bg.correct.R
inst/tests/expression.values.R
inst/tests/normalize.methods.R
man
man/AffyBatch-class.Rd
man/AffyRNAdeg.Rd
man/MAplot.Rd
man/ProbeSet-class.Rd
man/ProgressBarText-class.Rd
man/SpikeIn.Rd
man/affy-deprecated.Rd
man/affy-options.Rd
man/affy.scalevalue.exprSet.Rd
man/barplot.ProbeSet.Rd
man/bg.adjust.Rd
man/bgc.Rd
man/cdfFromBioC.Rd
man/cdfenv.example.Rd
man/cleancdfname.Rd
man/debug.affy123.Rd
man/expresso.Rd
man/expressoWidget.Rd
man/fit.li.wong.Rd
man/generateExprSet-methods.Rd
man/generateExprVal-methods.Rd
man/generateExprVal.method.avgdiff.Rd
man/generateExprVal.method.playerout.Rd
man/hlog.Rd
man/justrma.Rd
man/list.celfiles.Rd
man/maffy.subset.Rd
man/mas5.Rd
man/mas5calls.Rd
man/merge.AffyBatch.Rd
man/mva.pairs.Rd
man/normalize-methods.Rd
man/normalize.constant.Rd
man/normalize.contrast.Rd
man/normalize.invariantset.Rd
man/normalize.loess.Rd
man/normalize.qspline.Rd
man/normalize.quantiles.Rd
man/normalize.quantiles.robust.Rd
man/pairs.AffyBatch.Rd
man/plot.ProbeSet.Rd
man/plot.density.Rd
man/plotLocation.Rd
man/pmcorrect.Rd
man/ppsetApply.Rd
man/probeMatch-methods.Rd
man/probeNames-methods.Rd
man/read.affybatch.Rd
man/read.probematrix.Rd
man/rma.Rd
man/setAffyOptions.Rd
man/summary.Rd
man/tukey.biweight.Rd
man/whatcdf.Rd
man/xy2indices.Rd
src
src/Makevars.in
src/Makevars.win
src/chipbackground.c
src/getall_locations.c
src/mas5calls.c
src/rma2.c
src/rma_common.c
src/rma_common.h
vignettes
vignettes/EWSnap.png
vignettes/affy.Rnw
vignettes/affy.bib
vignettes/builtinMethods.Rnw
vignettes/customMethods.Rnw
vignettes/image.png
vignettes/vim.Rnw
vignettes/widget1.ps
vignettes/widget2.ps
vignettes/widgetfilechooser.png
affy documentation built on May 20, 2017, 9:52 p.m.