Methods for Affymetrix Oligonucleotide Arrays


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Documentation for package `affy' version 1.8.1

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

$.AffyBatch Class AffyBatch
.setAffyOptions ~~function to set options ~~

-- A --

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

-- B --

barplot,ProbeSet-method Class ProbeSet
barplot.ProbeSet show a ProbeSet as barplots
bg.adjust Background ajustment (internal function)
bg.correct Background Correction
bg.correct,AffyBatch,character-method Class AffyBatch
bg.correct.mas Background Correction
bg.correct.none Background Correction
bg.correct.rma Background Correction
bg.correct.rma2 Background Correction
bg.parameters Background ajustment (internal function)
bgcorrect From raw probe intensities to expression values
boxplot,AffyBatch-method Class AffyBatch

-- C --

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

-- D --

debug.affy123 Debugging Flag

-- E --

express.summary.stat Compute a summary expression value from the probes intensities
express.summary.stat,ProbeSet,character,character-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

-- F --

fit.li.wong Fit Li and Wong Model to a Probe Set

-- G --

geneNames Class AffyBatch
geneNames,AffyBatch-method Class AffyBatch
geneNames<-,AffyBatch-method Class AffyBatch
generateExprSet-methods generate a set of expression values
generateExprSet.methods generate a set of expression values
generateExprVal Compute a summary expression value from the probes intensities
generateExprVal-methods Compute a summary expression value from the probes intensities
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
generateExprVal.methods Compute a summary expression value from the probes intensities
getCdfInfo Class AffyBatch
getCdfInfo,AffyBatch-method Class AffyBatch

-- H --

hist,AffyBatch-method Class AffyBatch
hlog Hybrid Log

-- I --

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

-- J --

just.rma Read CEL files into an AffyBatch
justRMA Read CEL files into an AffyBatch

-- L --

length,AffyBatch-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 Normalize arrays

-- M --

ma.plot Relative M vs. A plots
mapCdfName Clean Affymetrix's CDF name
MAplot Relative M vs. A plots
MAplot,AffyBatch-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,AffyBatch-method MAS 5.0 Absolute Detection
mas5calls,ProbeSet-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,AffyBatch-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,AffyBatch-method Class AffyBatch
mm,ProbeSet-method Class ProbeSet
mm<-,AffyBatch,ANY-method Class AffyBatch
mm<-,ProbeSet,matrix-method Class ProbeSet
mmindex Class AffyBatch
mmindex,AffyBatch-method Class AffyBatch
mva.pairs M vs. A Matrix

-- N --

ncol,AffyBatch-method Class AffyBatch
normalize Normalize - generic
normalize,AffyBatch-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 Invariante 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 Invariante Set normalization
normalize.loess Scale microarray data
normalize.methods Normalize Affymetrix Probe Level Data - methods
normalize.methods,AffyBatch-method Normalize Affymetrix Probe Level Data - methods
normalize.qspline Normalize arrays
normalize.quantiles Quantile Normalization
normalize.quantiles.robust Robust Quantile Normalization
nrow,AffyBatch-method Class AffyBatch

-- O --

open,ProgressBarText-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
plotLocation Plot a location on a cel image
pm Methods for accessing perfect matches and mismatches
pm,AffyBatch-method Class AffyBatch
pm,ProbeSet-method Class ProbeSet
pm<-,AffyBatch,ANY-method Class AffyBatch
pm<-,ProbeSet,matrix-method Class ProbeSet
pmcorrect PM Correction
pmindex Class AffyBatch
pmindex,AffyBatch-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,AffyBatch-method Class AffyBatch
probeNames-methods Methods for accessing the Probe Names
probes Class AffyBatch
probes,AffyBatch-method Class AffyBatch
probeset Class AffyBatch
probeset,AffyBatch-method Class AffyBatch
ProbeSet-class Class ProbeSet
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

-- S --

sampleNames,ProbeSet-method Class ProbeSet
show,AffyBatch-method Class AffyBatch
show,ProbeSet-method Class ProbeSet
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,ProgressBarText-method Class "ProgressBarText"

-- W --

whatcdf Find which CDF corresponds

-- X --

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

-- misc --

[,AffyBatch-method Class AffyBatch
[<-,AffyBatch-method Class AffyBatch
[[,AffyBatch-method Class AffyBatch