PreProcessing of Agilent 4x44 array data


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Documentation for package ‘Agi4x44PreProcess’ version 1.2.0

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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)