Set of functions extending the capability of affylmGUI package. This library provides a graphical interface allowing QC, filtering and statistical validation for single channel microarrays. Affymetrix 3' IVT, Human Gene 1.0 ST and exon arrays are actually implemented.


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Documentation for package `oneChannelGUI' version 1.2.2

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oneChannelGUI-package Set of functions extending the capability of affylmGUI package
AboutextendedaffylmGUI Starting oneChannelGUI package
addAnnLib Starting oneChannelGUI package
changeMenu Starting oneChannelGUI package
delPLM Deleting PLM object
dfMAplot MA and Volcano plots from data present in a limma derived topTable
ExportNormalizedExpressionValues Starting oneChannelGUI package
extractAffyids Extracting probe ids associated to a specific Gene Ontology term
GOenrichment Searching for Gene Ontology enriched terms within a set of differentially expressed genes
GOstatsHelp Starting oneChannelGUI package
initialize.extAffylmGUI Starting oneChannelGUI package
inspecting.one.splice.index Plotting on the profiles of splice indexes for a transcript cluster ID
inspecting.splice.index Plotting on a pdf file the profiles of splice indexes
intensityFilter intensity filtering with a mouse click
intronicBg Starting oneChannelGUI package
IPAlistFilter Filtering an expression set using a set of Entrez genes extracted from Ingenuity Pathways analysis (IPA)
iqrFilter Interquantile filtering with a mouse click
libraryFilesDir Starting oneChannelGUI package
listFilter Subsetting an expression set using a list of Affymetrix ids
masigpro The function executes maSigPro analysis
masigpro.edesign The function creates an edesign object needed to run maSigPro
masigpro.view The function allows the visualization of maSigPro results
maSigProHelp Starting oneChannelGUI package
ML.edesign The function creates an data frame containing the parameters useful for class prediction
myExpresso Running the affy expresso function with the widget
myPLM Using fitPLM function with a mouse click
NewLimmaFile Starting oneChannelGUI package
ocPlotHist Gene/Exon level density plots
ocPlotPCA Gene/Exon level density plots
oneChannelGUI Set of functions extending the capability of affylmGUI package
oneChannelGUI.start Starting oneChannelGUI package
oneChannelGUIHelp Starting oneChannelGUI package
OpenAFile Starting oneChannelGUI package
OpenALimmaFile Starting oneChannelGUI package
OpenExonandTargetsfiles Starting oneChannelGUI package
OpenExonFile Starting oneChannelGUI package
OpenExonProbeFile Starting oneChannelGUI package
OpenLargeFile Starting oneChannelGUI package
OpenLargefiles This function loads large data set made from tab delimited files
OpenLimmaFile Starting oneChannelGUI package
PLM.plots RLE and NUSE plots with a mouse click
plotGO Plotting parents of a GO term with few mouse click
PlotOptionsv1 A modified version of the function used in affyPLM library
rawpCheck Raw p-value distribution from limma analysis by a mouse click
sample.size.evaluation The function executes and plots results from ssize and delta fulction from the ssize packahe
sample.size.evaluation1 The function executes functions from the sizepower packahe
SaveAsLimmaFile Starting oneChannelGUI package
showDataset Grabbing info about the available expression set
showTopTable Modification of the function immplemented in affylmGUI to generate a topTable
siggenes The function executes SAM analysis implemented in siggenes bioconductor library
siggenesHelp Starting oneChannelGUI package
spliceIndex This function coverts the exon intenisty data in a slice index
targetWidget Widget to create a target file to load .CEL files
templA Generating a template A to be uploaded in Ingenuity Pathways analysis (IPA)
trainTest Creating a training set and a test set by a mouse click
VennDiagram Venn diagrams using two or three lists
whichKindOfArray Starting oneChannelGUI package