Entry: AffyBatch-class
Aliases: AffyBatch-class AffyBatch,ANY AffyBatch probes geneNames geneNames<- getCdfInfo image indexProbes intensity<- intensity pmindex mmindex probeset $.AffyBatch cdfName cdfName,AffyBatch-method probes,AffyBatch-method geneNames,AffyBatch-method geneNames<-,AffyBatch,ANY-method geneNames<-,AffyBatch,ANY-method getCdfInfo,AffyBatch-method image,AffyBatch-method indexProbes,AffyBatch-method intensity<-,AffyBatch-method intensity,AffyBatch-method pmindex,AffyBatch-method mmindex,AffyBatch-method probeset,AffyBatch-method boxplot,AffyBatch-method nrow,AffyBatch-method ncol,AffyBatch-method show,AffyBatch-method pm,AffyBatch-method pm<-,AffyBatch,ANY-method mm,AffyBatch-method mm<-,AffyBatch,ANY-method probeNames,AffyBatch-method hist,AffyBatch-method [<-,AffyBatch-method [,AffyBatch-method [[,AffyBatch-method length,AffyBatch-method bg.correct,AffyBatch,character-method indexProbes,AffyBatch,character-method indexProbes,AffyBatch,missing-method computeExprSet,AffyBatch,character,character-method cdfName,AffyBatch-method
Keywords: classes
Description: Class AffyBatch
URL: ../../../library/affy/html/AffyBatch-class.html

Entry: AffyRNAdeg
Aliases: AffyRNAdeg summaryAffyRNAdeg plotAffyRNAdeg
Keywords: hplot manip
Description: Function to assess RNA degradation in Affymetrix GeneChip data.
URL: ../../../library/affy/html/AffyRNAdeg.html

Entry: MAplot
Aliases: ma.plot Mbox MAplot Mbox,AffyBatch-method MAplot,AffyBatch-method
Keywords: hplot
Description: Relative M vs. A plots
URL: ../../../library/affy/html/MAplot.html

Entry: ProbeSet-class
Aliases: ProbeSet-class mm,ProbeSet-method mm<-,ProbeSet,matrix-method pm<-,ProbeSet,matrix-method pm,ProbeSet-method show,ProbeSet-method barplot,ProbeSet-method colnames,ProbeSet-method express.summary.stat,ProbeSet,character,character-method sampleNames,ProbeSet-method
Keywords: classes
Description: Class ProbeSet
URL: ../../../library/affy/html/ProbeSet-class.html

Entry: ProgressBarText-class
Aliases: ProgressBarText-class close,ProgressBarText-method initialize,ProgressBarText-method open,ProgressBarText-method update,ProgressBarText-method
Keywords: classes
Description: Class "ProgressBarText"
URL: ../../../library/affy/html/ProgressBarText-class.html

Entry: SpikeIn
Aliases: SpikeIn concentrations
Keywords: datasets
Description: SpikeIn Experiment Data: ProbeSet Example
URL: ../../../library/affy/html/SpikeIn.html

Entry: affy-options
Aliases: affy-options
Keywords: manip
Description: Options for the affy package
URL: ../../../library/affy/html/affy-options.html

Entry: affy.scalevalue.exprSet
Aliases: affy.scalevalue.exprSet
Keywords: manip
Description: Scale normalization for expreSets
URL: ../../../library/affy/html/affy.scalevalue.exprSet.html

Entry: affybatch.example
Aliases: affybatch.example affybatch.example2
Keywords: methods
Description: AffyBatch instance affybatch.example
URL: ../../../library/affy/html/affybatch.example.html

Entry: barplot.ProbeSet
Aliases: barplot.ProbeSet
Keywords: hplot
Description: show a ProbeSet as barplots
URL: ../../../library/affy/html/barplot.ProbeSet.html

Entry: bg.adjust
Aliases: bg.adjust bg.parameters
Keywords: manip
Description: Background ajustment (internal function)
URL: ../../../library/affy/html/bg.adjust.html

Entry: bg.correct
Aliases: bg.correct bg.correct.none bg.correct.rma bg.correct.rma2 bg.correct.mas
Keywords: manip
Description: Background Correction
URL: ../../../library/affy/html/bgc.html

Entry: cdfFromBioC
Aliases: cdfFromBioC cdfFromData cdfFromLibPath cdfFromEnvironment
Keywords: utilities
Description: Functions to obtain CDF files
URL: ../../../library/affy/html/cdfFromBioC.html

Entry: cdfenv.example
Aliases: cdfenv.example
Keywords: datasets
Description: Example cdfenv
URL: ../../../library/affy/html/cdfenv.example.html

Entry: cleancdfname
Aliases: cleancdfname mapCdfName
Keywords: character
Description: Clean Affymetrix's CDF name
URL: ../../../library/affy/html/cleancdfname.html

Entry: debug.affy123
Aliases: debug.affy123
Keywords: methods
Description: Debugging Flag
URL: ../../../library/affy/html/debug.affy123.html

Entry: expresso
Aliases: expresso bgcorrect.methods bgcorrect
Keywords: manip
Description: From raw probe intensities to expression values
URL: ../../../library/affy/html/expresso.html

Entry: expressoWidget
Aliases: expressoWidget
Keywords: interface
Description: A widget for users to pick correction methods
URL: ../../../library/affy/html/expressoWidget.html

Entry: fit.li.wong
Aliases: fit.li.wong li.wong
Keywords: manip models
Description: Fit Li and Wong Model to a Probe Set
URL: ../../../library/affy/html/fit.li.wong.html

Entry: generateExprSet-method
Aliases: generateExprSet-methods computeExprSet generateExprSet.methods
Keywords: manip
Description: generate a set of expression values
URL: ../../../library/affy/html/generateExprSet-methods.html

Entry: generateExprVal
Aliases: generateExprVal generateExprVal-methods generateExprVal.methods express.summary.stat express.summary.stat-methods express.summary.stat.methods
Keywords: 
Description: Compute a summary expression value from the probes intensities
URL: ../../../library/affy/html/generateExprVal-methods.html

Entry: generateExprVal.method.avgdiff
Aliases: generateExprVal.method.avgdiff generateExprVal.method.medianpolish generateExprVal.method.liwong generateExprVal.method.mas
Keywords: manip
Description: Generate an expression value from the probes informations
URL: ../../../library/affy/html/generateExprVal.method.avgdiff.html

Entry: generateExprVal.method.playerout
Aliases: generateExprVal.method.playerout playerout.costfunction
Keywords: manip
Description: Generate an expression value from the probes informations
URL: ../../../library/affy/html/generateExprVal.method.playerout.html

Entry: hlog
Aliases: hlog
Keywords: math
Description: Hybrid Log
URL: ../../../library/affy/html/hlog.html

Entry: justRMA
Aliases: justRMA just.rma
Keywords: manip
Description: Read CEL files into an exprSet
URL: ../../../library/affy/html/justrma.html

Entry: list.celfiles
Aliases: list.celfiles
Keywords: character
Description: List the Cel Files in a Directory/Folder
URL: ../../../library/affy/html/list.celfiles.html

Entry: loess.normalize
Aliases: loess.normalize
Keywords: smooth
Description: Normalize arrays
URL: ../../../library/affy/html/loess.normalize.html

Entry: maffy.normalize
Aliases: maffy.normalize normalize.contrast
Keywords: internal
Description: Normalize Itensities
URL: ../../../library/affy/html/maffy.normalise.html

Entry: maffy.subset
Aliases: maffy.subset
Keywords: internal
Description: Select Subset
URL: ../../../library/affy/html/maffy.subset.html

Entry: mas5
Aliases: mas5
Keywords: manip
Description: MAS 5.0 expression measure
URL: ../../../library/affy/html/mas5.html

Entry: mas5calls
Aliases: mas5calls,AffyBatch-method mas5calls,ProbeSet-method mas5calls mas5.detection mas5calls.AffyBatch mas5calls.ProbeSet
Keywords: manip
Description: MAS 5.0 Absolute Detection
URL: ../../../library/affy/html/mas5calls.html

Entry: merge.AffyBatch
Aliases: merge.AffyBatch
Keywords: manip
Description: merge two AffyBatch objects
URL: ../../../library/affy/html/merge.AffyBatch.html

Entry: multiloess
Aliases: multiloess
Keywords: internal
Description: Local Polynomial Regression Fitting
URL: ../../../library/affy/html/multiloess.html

Entry: mva.pairs
Aliases: mva.pairs
Keywords: hplot
Description: M vs. A Matrix
URL: ../../../library/affy/html/mva.pairs.html

Entry: normalize-methods
Aliases: normalize.AffyBatch normalize.methods normalize.AffyBatch.methods normalize,AffyBatch-method normalize.methods,AffyBatch-method
Keywords: manip
Description: Normalize Affymetrix Probe Level Data - methods
URL: ../../../library/affy/html/normalize-methods.html

Entry: normalize
Aliases: normalize
Keywords: models
Description: Normalize - generic
URL: ../../../library/affy/html/normalize.html

Entry: normalize.constant
Aliases: normalize.constant normalize.AffyBatch.constant
Keywords: manip
Description: Scale probe intensities
URL: ../../../library/affy/html/normalize.constant.html

Entry: normalize.contrasts
Aliases: normalize.contrasts normalize.AffyBatch.contrasts
Keywords: manip
Description: Normalize intensities using the contrasts method
URL: ../../../library/affy/html/normalize.contrast.html

Entry: normalize.invariantset
Aliases: normalize.invariantset normalize.AffyBatch.invariantset
Keywords: manip
Description: Invariante Set normalization
URL: ../../../library/affy/html/normalize.invariantset.html

Entry: normalize.loess
Aliases: normalize.loess normalize.AffyBatch.loess
Keywords: smooth
Description: Scale microarray data
URL: ../../../library/affy/html/normalize.loess.html

Entry: normalize.qspline
Aliases: qspline-normalize normalize.qspline normalize.AffyBatch.qspline
Keywords: 
Description: Normalize arrays
URL: ../../../library/affy/html/normalize.qspline.html

Entry: normalize.quantiles
Aliases: normalize.quantiles normalize.AffyBatch.quantiles
Keywords: manip
Description: Quantile Normalization
URL: ../../../library/affy/html/normalize.quantiles.html

Entry: normalize.quantiles.robust
Aliases: normalize.quantiles.robust normalize.AffyBatch.quantiles.robust
Keywords: manip
Description: Robust Quantile Normalization
URL: ../../../library/affy/html/normalize.quantiles.robust.html

Entry: pairs.AffyBatch
Aliases: pairs.AffyBatch
Keywords: hplot
Description: plot intensities using 'pairs'
URL: ../../../library/affy/html/pairs.AffyBatch.html

Entry: plot.ProbeSet
Aliases: plot.ProbeSet
Keywords: hplot
Description: plot a probe set
URL: ../../../library/affy/html/plot.ProbeSet.html

Entry: plotDensity
Aliases: plotDensity plotDensity.AffyBatch
Keywords: hplot
Description: Plot Densities
URL: ../../../library/affy/html/plot.density.html

Entry: plotLocation
Aliases: plotLocation
Keywords: aplot
Description: Plot a location on a cel image
URL: ../../../library/affy/html/plotLocation.html

Entry: pmcorrect
Aliases: pmcorrect pmcorrect.methods pmcorrect.pmonly pmcorrect.mas pmcorrect.subtractmm
Keywords: manip
Description: PM Correction
URL: ../../../library/affy/html/pmcorrect.html

Entry: ppsetApply
Aliases: ppsetApply ppset.ttest
Keywords: manip
Description: Apply a function over the ProbeSets in an AffyBatch
URL: ../../../library/affy/html/ppsetApply.html

Entry: probeMatch-methods
Aliases: probeMatch-methods probeMatch pm pm<- mm mm<-
Keywords: methods
Description: Methods for accessing perfect matches and mismatches
URL: ../../../library/affy/html/probeMatch-methods.html

Entry: probeNames-methods
Aliases: probeNames-methods probeNames probeNames<-
Keywords: methods
Description: Methods for accessing the Probe Names
URL: ../../../library/affy/html/probeNames-methods.html

Entry: read.affybatch
Aliases: read.affybatch AllButCelsForReadAffy ReadAffy
Keywords: manip
Description: Read CEL files into an AffyBatch
URL: ../../../library/affy/html/read.affybatch.html

Entry: read.probematrix
Aliases: read.probematrix
Keywords: manip
Description: Read CEL file data into PM or MM matrices
URL: ../../../library/affy/html/read.probematrix.html

Entry: rma
Aliases: rma
Keywords: manip
Description: Robust Multi-Array Average expression measure
URL: ../../../library/affy/html/rma.html

Entry: .setAffyOptions
Aliases: .setAffyOptions
Keywords: manip
Description: ~~function to set options ~~
URL: ../../../library/affy/html/setAffyOptions.html

Entry: simplemultiLoess
Aliases: simplemultiLoess
Keywords: internal
Description: Internal function for multiloess
URL: ../../../library/affy/html/simplemultiLoess.html

Entry: summary
Aliases: summary medianpolish tukeybiweight avdiff
Keywords: manip
Description: Probe Set Summarizing Functions
URL: ../../../library/affy/html/summary.html

Entry: tukey.biweight
Aliases: tukey.biweight
Keywords: manip
Description: One-step Tukey's biweight
URL: ../../../library/affy/html/tukey.biweight.html

Entry: whatcdf
Aliases: whatcdf
Keywords: manip
Description: Find which CDF corresponds
URL: ../../../library/affy/html/whatcdf.html

Entry: xy2indices
Aliases: xy2indices indices2xy
Keywords: manip
Description: Functions to convert indices to x/y (and reverse)
URL: ../../../library/affy/html/xy2indices.html