\title{Starting oneChannelGUI package}

\name{oneChannelGUI}

\alias{AboutextendedaffylmGUI}
\alias{AboutaffylmGUI}
\alias{maSigProHelp}
\alias{siggenesHelp}
\alias{oneChannelGUIHelp}
\alias{initialize.extAffylmGUI}
\alias{OpenExonandTargetsfiles}
\alias{GOstatsHelp}
\alias{oneChannelGUIHelp}
\alias{NewLimmaFile}
\alias{OpenAFile}
\alias{OpenALimmaFile}
\alias{OpenLimmaFile}
\alias{OpenExonFile}
\alias{OpenExonProbeFile}
\alias{OpenLargeFile}
\alias{changeMenu}
\alias{oneChannelGUI.start}
\alias{libraryFilesDir}
\alias{whichKindOfArray}
\alias{intronicBg}
\alias{ExportNormalizedExpressionValues1}
\alias{ExportNormalizedExpressionValues}
\alias{ExportfeatureNames}
\alias{SaveAsLimmaFile}
\alias{addAnnLib}
\alias{OpenCDFandTargetsfiles}
\alias{ComputeLinearModelFit}
\alias{GetNormalizationMethod}
\alias{NormalizeNow}
\alias{ComputeContrasts}
\alias{midasFilter}
\alias{dabgFilter}
\alias{largedatasetNorm}
\alias{RankProdHelp}
\alias{affyPLMHelp}
\alias{genefilterHelp}
\alias{pamrHelp}
\alias{pdmclassHelp}
\alias{sizepowerHelp}
\alias{ssizeHelp}
\alias{OpenAGeoFile}
\alias{OpenGeoFile}
\alias{OpenGeoFiles}
\alias{recoverUnfiltered}
\alias{delete.ML}
\alias{affyPlotMA}
\alias{changes}
\alias{aptFolder}
\alias{deleteLocalData}
\alias{SetED}
\alias{chooseEDir}
\alias{.annotation}


\description{Starting oneChannelGUI package. oneChannelGUI contains a set of functions extending the 
capabilities of affylmGUI package}


\usage{
AboutextendedaffylmGUI()
AboutaffylmGUI()
oneChannelGUI()
oneChannelGUIHelp()
maSigProHelp()
siggenesHelp()
oneChannelGUIHelp()
initialize.extAffylmGUI()
OpenExonandTargetsfiles()
GOstatsHelp()
NewLimmaFile()
OpenLimmaFile()
OpenALimmaFile(FileName)
OpenAFile(FileName)
OpenExonFile()
OpenLargeFile()
changeMenu()
oneChannelGUI.start()
libraryFilesDir()
whichKindOfArray()
intronicBg()
ExportNormalizedExpressionValues1()
ExportNormalizedExpressionValues()
ExportfeatureNames()
SaveAsLimmaFile()
addAnnLib()
OpenCDFandTargetsfiles()
ComputeLinearModelFit()
GetNormalizationMethod()
NormalizeNow()
ComputeContrasts()
midasFilter()
dabgFilter()
largedatasetNorm()
RankProdHelp()
affyPLMHelp()
genefilterHelp()
pamrHelp()
pdmclassHelp()
sizepowerHelp()
ssizeHelp()
OpenAGeoFile(FileName)
OpenGeoFile()
OpenGeoFiles()
recoverUnfiltered()
delete.ML()
affyPlotMA()
changes()
aptFolder()
deleteLocalData()
SetED()
chooseEDir()
.annotation(eset)

}

\arguments{
\item{FileName}{Internal argument not to be set by the user}
\item{eset}{Internal argument not to be set by the user}
}

\details{
This function launches a modify version of the Graphical User Interface by James Wettenhall 
for the limma package by Gordon Smyth.
The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide
a simple interface to various tools for quality control and statistical analysis of Affymetrix gene chips.
}
\examples{
#  library(oneChannelGUI)
## To start the affylmGUI with the modifications
#oneChannelGUI()
}


\author{Raffaele A Calogero}

\keyword{IO}