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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) |