# Methods for Affymetrix Oligonucleotide Arrays

## Documentation for package ‘affy’ version 1.89.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P Q R S T U W X misc

## -- A --

affy-options | Options for the affy package
affy.scalevalue.exprSet | Scale normalization for expreSets
AffyBatch | Class AffyBatch
AffyBatch,ANY | Class AffyBatch
AffyBatch-class | Class AffyBatch
AffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data.
AllButCelsForReadAffy | Read CEL files into an AffyBatch
avdiff | Probe Set Summarizing Functions

## -- B --

barplot-method | Class ProbeSet
barplot.ProbeSet | show a ProbeSet as barplots
bg.adjust | Background adjustment (internal function)
bg.correct | Background Correction
bg.correct-method | Class AffyBatch
bg.correct.mas | Background Correction
bg.correct.none | Background Correction
bg.correct.rma | Background Correction
bg.parameters | Background adjustment (internal function)
bgcorrect | From raw probe intensities to expression values
bgcorrect.methods | Normalize Affymetrix Probe Level Data - methods
boxplot-method | Class AffyBatch

## -- C --

cdfenv.example | Example cdfenv
cdfFromBioC | Functions to obtain CDF files
cdfFromEnvironment | Functions to obtain CDF files
cdfFromLibPath | Functions to obtain CDF files
cdfName | Class AffyBatch
cdfName-method | Class AffyBatch
checkValidFilenames | Class AffyBatch
cleancdfname | Clean Affymetrix's CDF name
close-method | Class "ProgressBarText"
col-method | Class AffyBatch
colnames-method | Class ProbeSet
computeExprSet | generate a set of expression values
computeExprSet-method | Class AffyBatch
concentrations | SpikeIn Experiment Data: ProbeSet Example

## -- D --

debug.affy123 | Debugging Flag
dim-method | Class AffyBatch

## -- E --

express.summary.stat | Compute a summary expression value from the probes intensities
express.summary.stat-method | Class ProbeSet
express.summary.stat-methods | Compute a summary expression value from the probes intensities
express.summary.stat.methods | Compute a summary expression value from the probes intensities
expresso | From raw probe intensities to expression values
expressoWidget | A widget for users to pick correction methods
exprs-method | Class AffyBatch
exprs<--method | Class AffyBatch

## -- F --

featureNames-method | Class AffyBatch
featureNames<--method | Class AffyBatch
fit.li.wong | Fit Li and Wong Model to a Probe Set

## -- G --

geneNames | Class AffyBatch
geneNames-method | Class AffyBatch
geneNames<- | Class AffyBatch
geneNames<--method | Class AffyBatch
generateExprSet-methods | generate a set of expression values
generateExprSet.methods | generate a set of expression values
generateExprVal.method.avgdiff | Generate an expression value from the probes informations
generateExprVal.method.liwong | Generate an expression value from the probes informations
generateExprVal.method.mas | Generate an expression value from the probes informations
generateExprVal.method.medianpolish | Generate an expression value from the probes informations
generateExprVal.method.playerout | Generate an expression value from the probes informations
getCdfInfo | Class AffyBatch
getCdfInfo-method | Class AffyBatch

## -- H --

hist-method | Class AffyBatch
hlog | Hybrid Log

## -- I --

image | Class AffyBatch
image-method | Class AffyBatch
indexProbes | Class AffyBatch
indexProbes-method | Class AffyBatch
indices2xy | Functions to convert indices to x/y (and reverse)
initialize-method | Class AffyBatch
initialize-method | Class "ProgressBarText"
intensity | Class AffyBatch
intensity-method | Class AffyBatch
intensity<- | Class AffyBatch
intensity<--method | Class AffyBatch

## -- J --

just.rma | Read CEL files into an ExpressionSet
justRMA | Read CEL files into an ExpressionSet

## -- L --

length-method | Class AffyBatch
li.wong | Fit Li and Wong Model to a Probe Set
list.celfiles | List the Cel Files in a Directory/Folder
loess.normalize | Deprecated functions in package 'affy'

## -- M --

ma.plot | Relative M vs. A plots
maffy.normalize | Deprecated functions in package 'affy'
mapCdfName | Clean Affymetrix's CDF name
MAplot | Relative M vs. A plots
MAplot-method | Relative M vs. A plots
mas5 | MAS 5.0 expression measure
mas5.detection | MAS 5.0 Absolute Detection
mas5calls | MAS 5.0 Absolute Detection
mas5calls-method | MAS 5.0 Absolute Detection
mas5calls.AffyBatch | MAS 5.0 Absolute Detection
mas5calls.ProbeSet | MAS 5.0 Absolute Detection
Mbox | Relative M vs. A plots
Mbox-method | Relative M vs. A plots
medianpolish | Probe Set Summarizing Functions
merge.AffyBatch | merge two AffyBatch objects
mm | Methods for accessing perfect matches and mismatches
mm-method | Class AffyBatch
mm-method | Class ProbeSet
mm<- | Methods for accessing perfect matches and mismatches
mm<--method | Class AffyBatch
mm<--method | Class ProbeSet
mmindex | Class AffyBatch
mmindex-method | Class AffyBatch
multiloess | Deprecated functions in package 'affy'
mva.pairs | M vs. A Matrix

## -- N --

normalize-method | Normalize Affymetrix Probe Level Data - methods
normalize.AffyBatch | Normalize Affymetrix Probe Level Data - methods
normalize.AffyBatch.constant | Scale probe intensities
normalize.AffyBatch.contrasts | Normalize intensities using the contrasts method
normalize.AffyBatch.invariantset | Invariant Set normalization
normalize.AffyBatch.loess | Scale microarray data
normalize.AffyBatch.methods | Normalize Affymetrix Probe Level Data - methods
normalize.AffyBatch.qspline | Normalize arrays
normalize.AffyBatch.quantiles | Quantile Normalization
normalize.AffyBatch.quantiles.robust | Robust Quantile Normalization
normalize.constant | Scale probe intensities
normalize.contrasts | 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.methods-method | Normalize Affymetrix Probe Level Data - methods
normalize.qspline | Normalize arrays

## -- O --

open-method | Class "ProgressBarText"

## -- P --

pairs.AffyBatch | plot intensities using 'pairs'
playerout.costfunction | Generate an expression value from the probes informations
plot.ProbeSet | plot a probe set
plotAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data.
plotDensity | Plot Densities
plotDensity.AffyBatch | Plot Densities
plotLocation | Plot a location on a cel image
pm | Methods for accessing perfect matches and mismatches
pm-method | Class AffyBatch
pm-method | Class ProbeSet
pm<- | Methods for accessing perfect matches and mismatches
pm<--method | Class AffyBatch
pm<--method | Class ProbeSet
pmcorrect | PM Correction
pmcorrect.mas | PM Correction
pmcorrect.methods | Normalize Affymetrix Probe Level Data - methods
pmcorrect.pmonly | PM Correction
pmcorrect.subtractmm | PM Correction
pmindex | Class AffyBatch
pmindex-method | Class AffyBatch
ppset.ttest | Apply a function over the ProbeSets in an AffyBatch
ppsetApply | Apply a function over the ProbeSets in an AffyBatch
probeMatch | Methods for accessing perfect matches and mismatches
probeMatch-methods | Methods for accessing perfect matches and mismatches
probeNames | Methods for accessing the Probe Names
probeNames-method | Class AffyBatch
probeNames-methods | Methods for accessing the Probe Names
probeNames<- | Methods for accessing the Probe Names
probes | Class AffyBatch
probes-method | Class AffyBatch
probeset | Class AffyBatch
ProbeSet-class | Class ProbeSet
probeset-method | Class AffyBatch
ProgressBarText-class | Class "ProgressBarText"

## -- Q --

qspline-normalize | Normalize arrays

## -- R --

read.affybatch | Read CEL files into an AffyBatch
read.probematrix | Read CEL file data into PM or MM matrices
ReadAffy | Read CEL files into an AffyBatch
rma | Robust Multi-Array Average expression measure
row-method | Class AffyBatch

## -- S --

sampleNames-method | Class ProbeSet
se.exprs-method | Class AffyBatch
se.exprs<--method | Class AffyBatch
show-method | Class AffyBatch
show-method | Class ProbeSet
simplemultiLoess | Deprecated functions in package 'affy'
SpikeIn | SpikeIn Experiment Data: ProbeSet Example
summary | Probe Set Summarizing Functions
summaryAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data.

## -- T --

tukey.biweight | One-step Tukey's biweight
tukeybiweight | Probe Set Summarizing Functions

## -- U --

upDate.bgcorrect.methods | Normalize Affymetrix Probe Level Data - methods
upDate.express.summary.stat.methods | Compute a summary expression value from the probes intensities
upDate.generateExprSet.methods | generate a set of expression values
upDate.normalize.AffyBatch.methods | Normalize Affymetrix Probe Level Data - methods
upDate.pmcorrect.methods | Normalize Affymetrix Probe Level Data - methods
updateMe | Class "ProgressBarText"
updateMe-method | Class "ProgressBarText"
updateObject-method | Class AffyBatch

## -- W --

whatcdf | Find which CDF corresponds

## -- X --

xy2indices | Functions to convert indices to x/y (and reverse)

## -- misc --

$.AffyBatch | Class AffyBatch
.setAffyOptions | ~~function to set options ~~
[-method | Class AffyBatch
[<--method | Class AffyBatch
[[-method | Class AffyBatch