# This package extends the capabilities of affylmGUI graphical interface.

## Documentation for package `oneChannelGUI' version 1.2.20

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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