Package: affy 1.83.0

Robert D. Shear

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.

Authors:Rafael A. Irizarry <[email protected]>, Laurent Gautier <[email protected]>, Benjamin Milo Bolstad <[email protected]>, and Crispin Miller <[email protected]> with contributions from Magnus Astrand <[email protected]>, Leslie M. Cope <[email protected]>, Robert Gentleman, Jeff Gentry, Conrad Halling <[email protected]>, Wolfgang Huber, James MacDonald <[email protected]>, Benjamin I. P. Rubinstein, Christopher Workman <[email protected]>, John Zhang

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NEWS

# Install 'affy' in R:

install.packages('affy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rafalab/affy/issues

Datasets:

SpikeIn - SpikeIn Experiment Data: ProbeSet Example
cdfenv.example - Example cdfenv
mapCdfName - Clean Affymetrix's CDF name

On BioConductor:affy-1.83.0(bioc 3.20)affy-1.82.0(bioc 3.19)

bioconductor-package

123 exports 7.85 score 6 dependencies 107 dependents 989 mentions

Last updated 2 months agofrom:44ce0b6e3c

Exports:.setAffyOptions $.AffyBatch affy.scalevalue.exprSet AffyRNAdeg AllButCelsForReadAffy avdiff barplot barplot.ProbeSet bg.adjust bg.correct bg.correct.mas bg.correct.none bg.correct.rma bg.parameters bgcorrect.methods boxplot cdfFromBioC cdfFromEnvironment cdfFromLibPath cdfName checkValidFilenames cleancdfname close computeExprSet debug.affy123 express.summary.stat express.summary.stat.methods expresso expressoWidget exprs exprs<-featureNames fit.li.wong geneNames generateExprSet.methods generateExprVal.method.avgdiff generateExprVal.method.liwong generateExprVal.method.mas generateExprVal.method.medianpolish generateExprVal.method.playerout getCdfInfo hist hlog image indexProbes indices2xy intensity intensity<-just.rma justRMA li.wong list.celfiles loess.normalize ma.plot maffy.normalize maffy.subset MAplot mas5 mas5.detection mas5calls mas5calls.AffyBatch mas5calls.ProbeSet Mbox medianpolish merge.AffyBatch mm mm<-mmindex multiloess mva.pairs normalize.AffyBatch.constant normalize.AffyBatch.contrasts normalize.AffyBatch.invariantset normalize.AffyBatch.loess normalize.AffyBatch.methods normalize.AffyBatch.qspline normalize.AffyBatch.quantiles normalize.AffyBatch.quantiles.robust normalize.constant normalize.invariantset normalize.loess normalize.methods normalize.qspline open pairs.AffyBatch playerout.costfunction plot.ProbeSet plotAffyRNAdeg plotDensity plotDensity.AffyBatch plotLocation pm pm<-pmcorrect.mas pmcorrect.methods pmcorrect.pmonly pmcorrect.subtractmm pmindex ppset.ttest ppsetApply probeNames probes probeset read.affybatch read.probematrix ReadAffy rma sampleNames se.exprs show simplemultiLoess summaryAffyRNAdeg tukey.biweight tukeybiweight upDate.bgcorrect.methods upDate.express.summary.stat.methods upDate.generateExprSet.methods upDate.normalize.AffyBatch.methods upDate.pmcorrect.methods updateMe updateObject whatcdf xy2indices

Dependencies:affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
~~function to set options ~~	.setAffyOptions
Deprecated functions in package 'affy'	loess.normalize maffy.normalize multiloess simplemultiLoess
Options for the affy package	affy-options
Scale normalization for expreSets	affy.scalevalue.exprSet
Class AffyBatch	$.AffyBatch AffyBatch AffyBatch,ANY AffyBatch-class bg.correct,AffyBatch,character-method boxplot,AffyBatch-method cdfName cdfName,AffyBatch-method checkValidFilenames col,AffyBatch-method computeExprSet,AffyBatch,character,character-method dim,AffyBatch-method exprs,AffyBatch-method exprs<-,AffyBatch,ANY-method featureNames,AffyBatch-method featureNames<-,AffyBatch-method geneNames geneNames,AffyBatch-method geneNames<- geneNames<-,AffyBatch,ANY-method getCdfInfo getCdfInfo,AffyBatch-method hist,AffyBatch-method image image,AffyBatch-method indexProbes indexProbes,AffyBatch,character-method indexProbes,AffyBatch,missing-method indexProbes,AffyBatch-method initialize,AffyBatch-method intensity intensity,AffyBatch-method intensity<- intensity<-,AffyBatch-method length,AffyBatch-method mm,AffyBatch-method mm<-,AffyBatch,ANY-method mmindex mmindex,AffyBatch-method pm,AffyBatch-method pm<-,AffyBatch,ANY-method pmindex pmindex,AffyBatch-method probeNames,AffyBatch-method probes probes,AffyBatch-method probeset probeset,AffyBatch-method row,AffyBatch-method se.exprs,AffyBatch-method se.exprs<-,AffyBatch-method show,AffyBatch-method updateObject,AffyBatch-method [,AffyBatch-method [<-,AffyBatch-method [[,AffyBatch-method
Function to assess RNA degradation in Affymetrix GeneChip data.	AffyRNAdeg plotAffyRNAdeg summaryAffyRNAdeg
show a ProbeSet as barplots	barplot.ProbeSet
Background adjustment (internal function)	bg.adjust bg.parameters
Background Correction	bg.correct bg.correct.mas bg.correct.none bg.correct.rma
Example cdfenv	cdfenv.example
Functions to obtain CDF files	cdfFromBioC cdfFromEnvironment cdfFromLibPath
Clean Affymetrix's CDF name	cleancdfname mapCdfName
Debugging Flag	debug.affy123
From raw probe intensities to expression values	bgcorrect expresso
A widget for users to pick correction methods	expressoWidget
Fit Li and Wong Model to a Probe Set	fit.li.wong li.wong
generate a set of expression values	computeExprSet generateExprSet-methods generateExprSet.methods upDate.generateExprSet.methods
Compute a summary expression value from the probes intensities	express.summary.stat express.summary.stat-methods express.summary.stat.methods upDate.express.summary.stat.methods
Generate an expression value from the probes informations	generateExprVal.method.avgdiff generateExprVal.method.liwong generateExprVal.method.mas generateExprVal.method.medianpolish
Generate an expression value from the probes informations	generateExprVal.method.playerout playerout.costfunction
Hybrid Log	hlog
Read CEL files into an ExpressionSet	just.rma justRMA
List the Cel Files in a Directory/Folder	list.celfiles
Relative M vs. A plots	ma.plot MAplot MAplot,AffyBatch-method Mbox Mbox,AffyBatch-method
MAS 5.0 expression measure	mas5
MAS 5.0 Absolute Detection	mas5.detection mas5calls mas5calls,AffyBatch-method mas5calls,ProbeSet-method mas5calls.AffyBatch mas5calls.ProbeSet
merge two AffyBatch objects	merge.AffyBatch
M vs. A Matrix	mva.pairs
Normalize Affymetrix Probe Level Data - methods	bgcorrect.methods normalize,AffyBatch-method normalize.AffyBatch normalize.AffyBatch.methods normalize.methods normalize.methods,AffyBatch-method pmcorrect.methods upDate.bgcorrect.methods upDate.normalize.AffyBatch.methods upDate.pmcorrect.methods
Scale probe intensities	normalize.AffyBatch.constant normalize.constant
Normalize intensities using the contrasts method	normalize.AffyBatch.contrasts normalize.contrasts
Invariant Set normalization	normalize.AffyBatch.invariantset normalize.invariantset
Scale microarray data	normalize.AffyBatch.loess normalize.loess
Normalize arrays	normalize.AffyBatch.qspline normalize.qspline qspline-normalize
Quantile Normalization	normalize.AffyBatch.quantiles
Robust Quantile Normalization	normalize.AffyBatch.quantiles.robust
plot intensities using 'pairs'	pairs.AffyBatch
plot a probe set	plot.ProbeSet
Plot Densities	plotDensity plotDensity.AffyBatch
Plot a location on a cel image	plotLocation
PM Correction	pmcorrect pmcorrect.mas pmcorrect.pmonly pmcorrect.subtractmm
Apply a function over the ProbeSets in an AffyBatch	ppset.ttest ppsetApply
Methods for accessing perfect matches and mismatches	mm mm<- pm pm<- probeMatch probeMatch-methods
Methods for accessing the Probe Names	probeNames probeNames-methods probeNames<-
Class ProbeSet	barplot,ProbeSet-method colnames,ProbeSet-method express.summary.stat,ProbeSet,character,character-method mm,ProbeSet-method mm<-,ProbeSet,matrix-method pm,ProbeSet-method pm<-,ProbeSet,matrix-method ProbeSet-class sampleNames,ProbeSet-method show,ProbeSet-method
Class "ProgressBarText"	close,ProgressBarText-method initialize,ProgressBarText-method open,ProgressBarText-method ProgressBarText-class updateMe updateMe,ProgressBarText-method
Read CEL files into an AffyBatch	AllButCelsForReadAffy read.affybatch ReadAffy
Read CEL file data into PM or MM matrices	read.probematrix
Robust Multi-Array Average expression measure	rma
SpikeIn Experiment Data: ProbeSet Example	concentrations SpikeIn
Probe Set Summarizing Functions	avdiff medianpolish summary tukeybiweight
One-step Tukey's biweight	tukey.biweight
Find which CDF corresponds	whatcdf
Functions to convert indices to x/y (and reverse)	indices2xy xy2indices