Entry: Agi4x44PreProcess-package
Aliases: Agi4x44PreProcess-package Agi4x44PreProcess
Keywords: package
Description: PreProcessing of Agilent 4x44 array data
URL: ../../../library/Agi4x44PreProcess/html/Agi4x44PreProcess-package.html

Entry: BGandNorm
Aliases: BGandNorm
Keywords: documentation utilities
Description: Background Correction and Normalization Between Arrays
URL: ../../../library/Agi4x44PreProcess/html/BGandNorm.html

Entry: BoxPlot
Aliases: BoxPlot
Keywords: documentation utilities
Description: Boxplot
URL: ../../../library/Agi4x44PreProcess/html/BoxPlot.html

Entry: CV.rep.probes
Aliases: CV.rep.probes
Keywords: documentation utilities
Description: Non-control replicated Probes identication
URL: ../../../library/Agi4x44PreProcess/html/CV.rep.probes.html

Entry: HeatMap
Aliases: HeatMap
Keywords: documentation utilities
Description: HeatMap
URL: ../../../library/Agi4x44PreProcess/html/HeatMap.html

Entry: MVAplotMED
Aliases: MVAplotMED
Keywords: documentation utilities
Description: MVA plot
URL: ../../../library/Agi4x44PreProcess/html/MVAplotMED.html

Entry: MVAplotMEDctrl
Aliases: MVAplotMEDctrl
Keywords: documentation utilities
Description: MVA plot
URL: ../../../library/Agi4x44PreProcess/html/MVAplotMEDctrl.html

Entry: PCAplot
Aliases: PCAplot
Keywords: documentation utilities
Description: PCA plot
URL: ../../../library/Agi4x44PreProcess/html/PCAplot.html

Entry: RLE
Aliases: RLE
Keywords: documentation utilities
Description: Relative Log Expression
URL: ../../../library/Agi4x44PreProcess/html/RLE.html

Entry: boxplotNegCtrl
Aliases: boxplotNegCtrl
Keywords: documentation utilities
Description: Boxplot of Signals and Negative Controls
URL: ../../../library/Agi4x44PreProcess/html/boxplotNegCtrl.html

Entry: build.eset
Aliases: build.eset
Keywords: documentation utilities
Description: ExpressionSet object from a RGList
URL: ../../../library/Agi4x44PreProcess/html/build.eset.html

Entry: build.mappings
Aliases: build.mappings
Keywords: documentation utilities
Description: Creates data.frame with information mapped from the annotation package
URL: ../../../library/Agi4x44PreProcess/html/build.mappings.html

Entry: countFLAG
Aliases: countFLAG
Keywords: documentation utilities
Description: filter.probes (internal function)
URL: ../../../library/Agi4x44PreProcess/html/countFLAG.html

Entry: dd
Aliases: dd
Keywords: datasets
Description: data example (RGList)
URL: ../../../library/Agi4x44PreProcess/html/dd.html

Entry: ensembl.htmlpage
Aliases: ensembl.htmlpage
Keywords: documentation utilities
Description: genes.rpt.agi (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/ensembl.htmlpage.html

Entry: filter.NonUnifOL
Aliases: filter.NonUnifOL
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.NonUnifOL.html

Entry: filter.PopnOL
Aliases: filter.PopnOL
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.PopnOL.html

Entry: filter.control
Aliases: filter.control
Keywords: documentation utilities
Description: filter.probes (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.control.html

Entry: filter.isfound
Aliases: filter.isfound
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.isfound.html

Entry: filter.nas
Aliases: filter.nas
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.nas.html

Entry: filter.probes
Aliases: filter.probes
Keywords: documentation utilities
Description: Filtering out probes
URL: ../../../library/Agi4x44PreProcess/html/filter.probes.html

Entry: filter.saturated
Aliases: filter.saturated
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.saturated.html

Entry: filter.wellaboveBG
Aliases: filter.wellaboveBG
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.wellaboveBG.html

Entry: filter.wellaboveNEG
Aliases: filter.wellaboveNEG
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filter.wellaboveNEG.html

Entry: filterFLAG
Aliases: filterFLAG
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filterFLAG.html

Entry: filterFLAGall
Aliases: filterFLAGall
Keywords: documentation utilities
Description: filter.probes (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filterFLAGall.html

Entry: filterNAS
Aliases: filterNAS
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filterNAS.html

Entry: filterWellAboveSIGNALv2
Aliases: filterWellAboveSIGNALv2
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/filterWellAboveSIGNALv2.html

Entry: genes.rpt.agi
Aliases: genes.rpt.agi
Keywords: documentation utilities
Description: Genes interrogated for different probes
URL: ../../../library/Agi4x44PreProcess/html/genes.rpt.agi.html

Entry: getTDRows3
Aliases: getTDRows3
Keywords: documentation utilities
Description: ensembl.htmlpage: (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/getTDRows3.html

Entry: gsea.files
Aliases: gsea.files
Keywords: documentation utilities
Description: Creates files for GSEA
URL: ../../../library/Agi4x44PreProcess/html/gsea.files.html

Entry: hierclus
Aliases: hierclus
Keywords: documentation utilities
Description: Hierarchical clustering
URL: ../../../library/Agi4x44PreProcess/html/hierclus.html

Entry: paste.character
Aliases: paste.character
Keywords: documentation utilities
Description: paste characters (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/paste.character.html

Entry: plotDensity
Aliases: plotDensity
Keywords: documentation utilities
Description: Density Plots of Intensity Signals
URL: ../../../library/Agi4x44PreProcess/html/plotDensity.html

Entry: read.AgilentFE
Aliases: read.AgilentFE
Keywords: documentation utilities
Description: Read Agilent Feature Extraction *.txt data files
URL: ../../../library/Agi4x44PreProcess/html/read.AgilentFE.html

Entry: read.targets
Aliases: read.targets
Keywords: documentation utilities
Description: read the target file
URL: ../../../library/Agi4x44PreProcess/html/read.targets.html

Entry: subCHR
Aliases: subCHR
Keywords: documentation utilities
Description: chr coordinates edition (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/subCHR.html

Entry: summarize.probe
Aliases: summarize.probe
Keywords: documentation utilities
Description: Replicated Probes Summarization
URL: ../../../library/Agi4x44PreProcess/html/summarize.probe.html

Entry: targets
Aliases: targets
Keywords: datasets
Description: Example of target file
URL: ../../../library/Agi4x44PreProcess/html/targets.html

Entry: write.control.out
Aliases: write.control.out
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/write.control.out.html

Entry: write.eset
Aliases: write.eset
Keywords: documentation utilities
Description: Writes the expression data matrix of an ExpressionSet object in a file
URL: ../../../library/Agi4x44PreProcess/html/write.eset.html

Entry: write.filt.out
Aliases: write.filt.out
Keywords: documentation utilities
Description: probes.filter (Internal function)
URL: ../../../library/Agi4x44PreProcess/html/write.filt.out.html
