affy: Methods for Affymetrix Oligonucleotide Arrays

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

Author
Rafael 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 publication
None
Maintainer
Rafael A. Irizarry <rafa@jhu.edu>
License
LGPL (>= 2.0)
Version
1.52.0

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)

Files in this package

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