# PreProcessing of Agilent 4x44 array data

## Documentation for package ‘Agi4x44PreProcess’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

Agi4x44PreProcess-package | PreProcessing of Agilent 4x44 array data
Agi4x44PreProcess | PreProcessing of Agilent 4x44 array data
BGandNorm | Background Correction and Normalization Between Arrays
BoxPlot | Boxplot
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)
CV.rep.probes | Non-control replicated Probes identication
dd | data example (RGList)
ensembl.htmlpage | genes.rpt.agi (Internal function)
filter.control | filter.probes (Internal function)
filter.isfound | probes.filter (Internal function)
filter.nas | probes.filter (Internal function)
filter.NonUnifOL | probes.filter (Internal function)
filter.PopnOL | 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
HeatMap | HeatMap
hierclus | Hierarchical clustering
MVAplotMED | MVA plot
MVAplotMEDctrl | MVA plot
paste.character | paste characters (Internal function)
PCAplot | PCA plot
plotDensity | Density Plots of Intensity Signals
read.AgilentFE | Read Agilent Feature Extraction *.txt data files
read.targets | read the target file
RLE | Relative Log Expression
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)