This package extends the capabilities of affylmGUI graphical interface.


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Documentation for package `oneChannelGUI' version 1.2.20

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oneChannelGUI-package Set of functions extending the capability of affylmGUI package
AboutaffylmGUI Starting oneChannelGUI package
AboutextendedaffylmGUI Starting oneChannelGUI package
addAnnLib Starting oneChannelGUI package
affyPLMHelp Starting oneChannelGUI package
affyPlotMA Starting oneChannelGUI package
AptMidas Graphical interface to APT midas
changeMenu Starting oneChannelGUI package
ComputeContrasts Starting oneChannelGUI package
ComputeLinearModelFit Starting oneChannelGUI package
crosshybFilter Removing from exon array gene/exon level probe sets characterized by cross hybridization with other transcripts
crosshybhuex10stv2na22hg18 Cross hybriduzation data for exon CORE subset of human exon array 1.0 ST
crosshybmoex10stv1na22mm8 Cross hybriduzation data for exon CORE subset of mouse exon array 1.0 ST
crosshybraex10stv1na22rn4 Cross hybriduzation data for exon CORE subset of rat exon array 1.0 ST
dabgFilter Starting oneChannelGUI package
delete.ML Starting oneChannelGUI package
dfMAplot MA and Volcano plots from data present in a limma derived topTable
erankProdAltSpl Implementation of the Rank Product method for the detection of alternative splicing events
erankProdAltSplFilter Filtering Rank Product results for the detection of alternative splicing events
ExportNormalizedExpressionValues Starting oneChannelGUI package
ExportNormalizedExpressionValues1 Starting oneChannelGUI package
extractAffyids Extracting probe ids associated to a specific Gene Ontology term
filteringTable Filtering a tab delimited file
genefilterHelp Starting oneChannelGUI package
geoVSbioc linking GEO platforms to available BioC annotations libraries
GetNormalizationMethod Starting oneChannelGUI package
GOenrichment Searching for Gene Ontology enriched terms within a set of differentially expressed genes
GOstatsHelp Starting oneChannelGUI package
huex10stv2na22hg18 Annotation data for CORE subset of human exon array 1.0 ST
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
largedatasetNorm Starting oneChannelGUI package
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
midasFilter Starting oneChannelGUI package
ML.edesign The function creates an data frame containing the parameters useful for class prediction
moex10stv1na22mm8 Annotation data for CORE subset of mouse exon array 1.0 ST
myExpresso Running the affy expresso function with the widget
NewLimmaFile Starting oneChannelGUI package
NormalizeNow 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
OpenAGeoFile Starting oneChannelGUI package
OpenALimmaFile Starting oneChannelGUI package
OpenCDFandTargetsfiles Starting oneChannelGUI package
OpenExonandTargetsfiles Starting oneChannelGUI package
OpenExonFile Starting oneChannelGUI package
OpenExonProbeFile Starting oneChannelGUI package
OpenGeoFile Starting oneChannelGUI package
OpenGeoFiles Starting oneChannelGUI package
OpenLargeFile Starting oneChannelGUI package
OpenLargefiles This function loads large data set made from tab delimited files
OpenLimmaFile Starting oneChannelGUI package
pamrHelp Starting oneChannelGUI package
pdmclassHelp Starting oneChannelGUI package
plierToZero Setting to 0 low log2 intensity values generated with plier
plotGO Plotting parents of a GO term with few mouse click
PlotOptionsv1 A modified version of the function used in affyPLM library
raex10stv1na22rn4 Annotation data for CORE subset of rat exon array 1.0 ST
rankProd graphical interface to rank product method implemented in RankProd Bioconductor library.
RankProdHelp Starting oneChannelGUI package
rawpCheck Raw p-value distribution from limma analysis by a mouse click
recoverUnfiltered Starting oneChannelGUI package
reviqrFilter Reverse interquantile filtering with 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
simFilter This function allows filtering on the basis of the average splice index mean difference between two groups
sizepowerHelp Starting oneChannelGUI package
spliceIndex This function coverts the exon intenisty data in a slice index
ssizeHelp Starting oneChannelGUI package
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