\HeaderA{oneChannelGUI}{Starting oneChannelGUI package}{oneChannelGUI}
\aliasA{.annotation}{oneChannelGUI}{.annotation}
\aliasA{.myrk}{oneChannelGUI}{.myrk}
\aliasA{AboutaffylmGUI}{oneChannelGUI}{AboutaffylmGUI}
\aliasA{AboutextendedaffylmGUI}{oneChannelGUI}{AboutextendedaffylmGUI}
\aliasA{addAnnLib}{oneChannelGUI}{addAnnLib}
\aliasA{affyPLMHelp}{oneChannelGUI}{affyPLMHelp}
\aliasA{affyPlotMA}{oneChannelGUI}{affyPlotMA}
\aliasA{aptFolder}{oneChannelGUI}{aptFolder}
\aliasA{changeMenu}{oneChannelGUI}{changeMenu}
\aliasA{changes}{oneChannelGUI}{changes}
\aliasA{chooseEDir}{oneChannelGUI}{chooseEDir}
\aliasA{ComputeContrasts}{oneChannelGUI}{ComputeContrasts}
\aliasA{ComputeLinearModelFit}{oneChannelGUI}{ComputeLinearModelFit}
\aliasA{dabgFilter}{oneChannelGUI}{dabgFilter}
\aliasA{delete.ML}{oneChannelGUI}{delete.ML}
\aliasA{deleteLocalData}{oneChannelGUI}{deleteLocalData}
\aliasA{ExportfeatureNames}{oneChannelGUI}{ExportfeatureNames}
\aliasA{ExportNormalizedExpressionValues}{oneChannelGUI}{ExportNormalizedExpressionValues}
\aliasA{ExportNormalizedExpressionValues1}{oneChannelGUI}{ExportNormalizedExpressionValues1}
\aliasA{genefilterHelp}{oneChannelGUI}{genefilterHelp}
\aliasA{GetNormalizationMethod}{oneChannelGUI}{GetNormalizationMethod}
\aliasA{GOstatsHelp}{oneChannelGUI}{GOstatsHelp}
\aliasA{initialize.extAffylmGUI}{oneChannelGUI}{initialize.extAffylmGUI}
\aliasA{intronicBg}{oneChannelGUI}{intronicBg}
\aliasA{largedatasetNorm}{oneChannelGUI}{largedatasetNorm}
\aliasA{libraryFilesDir}{oneChannelGUI}{libraryFilesDir}
\aliasA{maSigProHelp}{oneChannelGUI}{maSigProHelp}
\aliasA{midasFilter}{oneChannelGUI}{midasFilter}
\aliasA{NewLimmaFile}{oneChannelGUI}{NewLimmaFile}
\aliasA{NormalizeNow}{oneChannelGUI}{NormalizeNow}
\aliasA{oneChannelGUI.start}{oneChannelGUI}{oneChannelGUI.start}
\aliasA{oneChannelGUIHelp}{oneChannelGUI}{oneChannelGUIHelp}
\methaliasA{oneChannelGUIHelp}{oneChannelGUI}{oneChannelGUIHelp}
\aliasA{OpenAFile}{oneChannelGUI}{OpenAFile}
\aliasA{OpenAGeoFile}{oneChannelGUI}{OpenAGeoFile}
\aliasA{OpenALimmaFile}{oneChannelGUI}{OpenALimmaFile}
\aliasA{OpenCDFandTargetsfiles}{oneChannelGUI}{OpenCDFandTargetsfiles}
\aliasA{OpenExonandTargetsfiles}{oneChannelGUI}{OpenExonandTargetsfiles}
\aliasA{OpenExonFile}{oneChannelGUI}{OpenExonFile}
\aliasA{OpenExonProbeFile}{oneChannelGUI}{OpenExonProbeFile}
\aliasA{OpenGeoFile}{oneChannelGUI}{OpenGeoFile}
\aliasA{OpenGeoFiles}{oneChannelGUI}{OpenGeoFiles}
\aliasA{OpenLargeFile}{oneChannelGUI}{OpenLargeFile}
\aliasA{OpenLimmaFile}{oneChannelGUI}{OpenLimmaFile}
\aliasA{pamrHelp}{oneChannelGUI}{pamrHelp}
\aliasA{pdmclassHelp}{oneChannelGUI}{pdmclassHelp}
\aliasA{RankProdHelp}{oneChannelGUI}{RankProdHelp}
\aliasA{recoverUnfiltered}{oneChannelGUI}{recoverUnfiltered}
\aliasA{SaveAsLimmaFile}{oneChannelGUI}{SaveAsLimmaFile}
\aliasA{SetED}{oneChannelGUI}{SetED}
\aliasA{siggenesHelp}{oneChannelGUI}{siggenesHelp}
\aliasA{sizepowerHelp}{oneChannelGUI}{sizepowerHelp}
\aliasA{ssizeHelp}{oneChannelGUI}{ssizeHelp}
\aliasA{whichKindOfArray}{oneChannelGUI}{whichKindOfArray}
\keyword{IO}{oneChannelGUI}
\begin{Description}\relax
Starting oneChannelGUI package. oneChannelGUI contains a set of functions extending the 
capabilities of affylmGUI package
\end{Description}
\begin{Usage}
\begin{verbatim}
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)
.myrk(x,df)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{FileName}] Internal argument not to be set by the user
\item[\code{eset}] Internal argument not to be set by the user
\item[\code{x}] Internal argument not to be set by the user
\item[\code{df}] Internal argument not to be set by the user
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
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.
\end{Details}
\begin{Author}\relax
Raffaele A Calogero
\end{Author}
\begin{Examples}
\begin{ExampleCode}
#  library(oneChannelGUI)
## To start the affylmGUI with the modifications
#oneChannelGUI()
\end{ExampleCode}
\end{Examples}

