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)

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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