Agi4x44PreProcess-package
                        PreProcessing of Agilent 4x44 array data
BGandNorm               Background Correction and Normalization Between
                        Arrays
BoxPlot                 Boxplot
CV.rep.probes           Non-control replicated Probes identication
HeatMap                 HeatMap
MVAplotMED              MVA plot
MVAplotMEDctrl          MVA plot
PCAplot                 PCA plot
RLE                     Relative Log Expression
boxplotNegCtrl          Boxplot of Signals and Negative Controls
build.eset              ExpressionSet object from a RGList
build.mappings          Creates data.frame with information mapped from
                        the annotation package
countFLAG               filter.probes (internal function)
dd                      data example (RGList)
ensembl.htmlpage        genes.rpt.agi (Internal function)
filter.NonUnifOL        probes.filter (Internal function)
filter.PopnOL           probes.filter (Internal function)
filter.control          filter.probes (Internal function)
filter.isfound          probes.filter (Internal function)
filter.nas              probes.filter (Internal function)
filter.probes           Filtering out probes
filter.saturated        probes.filter (Internal function)
filter.wellaboveBG      probes.filter (Internal function)
filter.wellaboveNEG     probes.filter (Internal function)
filterFLAG              probes.filter (Internal function)
filterFLAGall           filter.probes (Internal function)
filterNAS               probes.filter (Internal function)
filterWellAboveSIGNALv2
                        probes.filter (Internal function)
genes.rpt.agi           Genes interrogated for different probes
getTDRows3              ensembl.htmlpage: (Internal function)
gsea.files              Creates files for GSEA
hierclus                Hierarchical clustering
paste.character         paste characters (Internal function)
plotDensity             Density Plots of Intensity Signals
read.AgilentFE          Read Agilent Feature Extraction *.txt data
                        files
read.targets            read the target file
subCHR                  chr coordinates edition (Internal function)
summarize.probe         Replicated Probes Summarization
targets                 Example of target file
write.control.out       probes.filter (Internal function)
write.eset              Writes the expression data matrix of an
                        ExpressionSet object in a file
write.filt.out          probes.filter (Internal function)
