Entry: FeatureSet-class
Aliases: FeatureSet-class allele,FeatureSet-method boxplot,FeatureSet-method featureIndex,FeatureSet-method geneNames,FeatureSet-method getPlatformDesign,FeatureSet-method hist,FeatureSet-method image,FeatureSet-method indexFeatureSetName,FeatureSet-method length,FeatureSet-method mmindex,FeatureSet-method mm<-,FeatureSet-method mm,FeatureSet-method ncol,FeatureSet-method npixels,FeatureSet-method nrow,FeatureSet-method platformDesignName,FeatureSet-method platform,FeatureSet-method pmindex,FeatureSet-method pm<-,FeatureSet-method pm,FeatureSet-method probeNames,FeatureSet-method sd,FeatureSet-method show,FeatureSet-method $.platformDesign, FeatureSet-method exprs, FeatureSet-method manufacturer, FeatureSet-method manufacturer<-, FeatureSet-method platform<-, FeatureSet-method
Keywords: classes
Description: Class "FeatureSet"
URL: ../../../library/oligo/html/FeatureSet-class.html

Entry: Methods for FeatureSet
Aliases: platform<-,FeatureSet-method manufacturer,FeatureSet-method manufacturer<-,FeatureSet-method exprs,FeatureSet-method initialize, FeatureSet-method probeNames, FeatureSet-method
Keywords: methods
Description: Methods for FeatureSet objects
URL: ../../../library/oligo/html/FeatureSet-methods.html

Entry: FeatureSet subclasses
Aliases: ExpressionFeatureSet-class SnpFeatureSet-class TilingFeatureSet-class
Keywords: classes
Description: Subclasses of FeatureSet.
URL: ../../../library/oligo/html/SubClasses.html

Entry: Accessors
Aliases: npixels type platform platform<- manufacturer manufacturer<-
Keywords: methods
Description: Accessors for FeatureSet objects.
URL: ../../../library/oligo/html/accessors.html

Entry: allele
Aliases: allele
Keywords: manip
Description: Retrieve allele from PDEnv for SNP arrays
URL: ../../../library/oligo/html/allele.html

Entry: as.data.frame.platformDesign
Aliases: as.data.frame.platformDesign
Keywords: manip
Description: Coerce to a Data Frame
URL: ../../../library/oligo/html/as.data.frame.platformDesign.html

Entry: Obtain the ATCG content of a gene
Aliases: basecontent
Keywords: methods
Description: Boxplot
URL: ../../../library/oligo/html/basecontent.html

Entry: bg.correct
Aliases: bg.correct.rma
Keywords: manip
Description: Background Correction
URL: ../../../library/oligo/html/bg.correct.html

Entry: characterOrNULL-class
Aliases: characterOrNULL-class
Keywords: classes
Description: Class "characterOrNULL"
URL: ../../../library/oligo/html/characterOrNULL-class.html

Entry: cleanPlatformName
Aliases: cleanPlatformName
Keywords: manip
Description: Naming PDEnvs
URL: ../../../library/oligo/html/cleanPlatformName.html

Entry: Array dimensions
Aliases: nrow
Keywords: methods
Description: Accessors for the dimensions of the array
URL: ../../../library/oligo/html/dimensions.html

Entry: featureIndex
Aliases: featureIndex
Keywords: manip
Description: Indexes of features on the array
URL: ../../../library/oligo/html/featureIndex.html

Entry: featureInfo
Aliases: featureInfo
Keywords: manip
Description: Platform Design Environment
URL: ../../../library/oligo/html/featureInfo.html

Entry: File Manipulation
Aliases: list.celfiles list.xysfiles
Keywords: manip
Description: Functions to list CEL and XYS files.
URL: ../../../library/oligo/html/fileManip.html

Entry: getPlatformDesign
Aliases: getPlatformDesign getPD
Keywords: methods
Description: Platform Design accessor
URL: ../../../library/oligo/html/getPlatformDesign.html

Entry: indexFeatureSetName
Aliases: indexFeatureSetName
Keywords: manip
Description: Indexes for feature sets.
URL: ../../../library/oligo/html/indexFeatureSetName.html

Entry: Conversion fro XY to Index
Aliases: i2xy xy2i
Keywords: manip
Description: Index <-> XY
URL: ../../../library/oligo/html/indexTools.html

Entry: initialize-methods
Aliases: initialize-methods initialize,ANY-method initialize,traceable-method initialize,signature-method initialize,environment-method initialize,AnnotatedDataFrame-method initialize,eSet-method initialize,ExpressionSet-method initialize,SnpSet-method initialize,FeatureSet-method
Keywords: methods
Description: Methods for Class Initialization
URL: ../../../library/oligo/html/initialize-methods.html

Entry: Methods for Sequences
Aliases: pmSequence mmSequence sequenceDesignMatrix
Keywords: methods
Description: Methods to deal with sequences.
URL: ../../../library/oligo/html/methods-Sequences.html

Entry: nProbes
Aliases: nProbes
Keywords: methods
Description: Number of probes on the array
URL: ../../../library/oligo/html/nProbes.html

Entry: names
Aliases: names
Keywords: methods
Description: Platform Design variables
URL: ../../../library/oligo/html/names.html

Entry: Quantile Normalization
Aliases: normalize.quantiles normalize.FeatureSet.quantiles
Keywords: methods
Description: Quantile Normalization Functions
URL: ../../../library/oligo/html/normalize.quantiles.html

Entry: File parsers
Aliases: read.xysfiles readonexysfile readxysHeader
Keywords: methods
Description: XYS files parser.
URL: ../../../library/oligo/html/parsers.html

Entry: platformDesign-class
Aliases: platformDesign-class mmindex,platformDesign-method names,platformDesign-method nProbes,platformDesign-method pmindex,platformDesign-method probeNames,platformDesign-method show,platformDesign-method $.platformDesign
Keywords: classes
Description: Class "platformDesign"
URL: ../../../library/oligo/html/platformDesign-class.html

Entry: platformDesignName
Aliases: platformDesignName
Keywords: manip
Description: The platform design object name.
URL: ../../../library/oligo/html/platformDesignName.html

Entry: Plot Densities
Aliases: plotDensity plotDensity.FeatureSet
Keywords: hplot
Description: Plot Densities
URL: ../../../library/oligo/html/plotDensity.html

Entry: probeMatch-methods
Aliases: pm mm pm<- mm<- pmindex mmindex
Keywords: methods
Description: Accessors for perfect match (pm) and mismatch (mm) probes.
URL: ../../../library/oligo/html/probeMatch-methods.html

Entry: probeNames-methods
Aliases: probeNames-methods probeNames,platformDesign,characterOrNULL-method probeNames,FeatureSet,characterOrNULL-method
Keywords: methods
Description: Probe Names
URL: ../../../library/oligo/html/probeNames-methods.html

Entry: probeNames
Aliases: probeNames
Keywords: manip
Description: Feature Set Names
URL: ../../../library/oligo/html/probeNames.html

Entry: File Parsers
Aliases: read.celfiles read.affybatch stuffForXYSandCELreaders
Keywords: manip
Description: Affymetrix CEL files parser
URL: ../../../library/oligo/html/read.celfiles.html

Entry: rma
Aliases: rma
Keywords: methods
Description: Robust multi-array average
URL: ../../../library/oligo/html/rma.html
