affy: Methods for Affymetrix Oligonucleotide Arrays

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

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
Date of publicationNone
MaintainerRafael A. Irizarry <rafa@jhu.edu>
LicenseLGPL (>= 2.0)
Version1.52.0

View on Bioconductor

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

Files

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

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