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%\VignetteKeywords{one channel microarray,extended Affymetrix GUI, limma, quality control, data filtering, time course}
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\begin{document}
\title{oneChannelGUI Package Installation}
\author{Raffaele A Calogero, Francesca Cordero, Remo Sanges}
\date{May 12 2011}
\maketitle

\section{Installation}
It is important to install additional software other than R and Bioconductor libraries, 
for the complete functionality of oneChannelGUI.

The external tools and data needed to run exon array analysis in oneChannelGUI are shown in figure \ref{fig:inst1}.

\begin{figure}[htbp]
  \begin{center}
    \includegraphics{inst1}
    \caption{\label{fig:inst1} External tools needed for exon array analysis when oneChannelGUI add-on is loaded in affylmGUI.}
  \end{center}
\end{figure}


\subsection{Windows users}
The lastest version of R need to be installed. It can be downloaded at:
\url{http://www.r-project.org/}
oneChannelGUI needs the installation of the following packages:
<<>>=
packageDescription("oneChannelGUI")$Depends
@
oneChannelGUI suggests the installation of the following packages:
<<>>=
packageDescription("oneChannelGUI")$Suggests
@

In order to install all the Bioconductor packages needed to run oneChannelGUI a 
specific R function can be downloaded from \url{http://www.bioinformatica.unito.it/oneChannelGUI/}
To use it user needs to open an R session on a computer connected to internet and 
copy and paste the following code:
\begin{Schunk}
\begin{Sinput}
source("http://bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi","affy","AffyCompatible","affylmGUI","affyPLM","annaffy","annotate","AnnotationDbi",
                "beadarray","Biobase","biomaRt","Biostrings", "IRanges","DynDoc","genefilter","geneplotter","GenomeGraphs",
                "GO.db","GOstats","graph","hugene10sttranscriptcluster.db","hgu133a.db","hgu133a2.db","hgu133a2cdf",
                "hgu133a2probe","hgu133acdf","hgu133aprobe","hgu133plus2.db","hgu133plus2cdf","hgu133plus2probe",
                "hgu95av2cdf","hgu95av2probe","hugene10sttranscriptcluster.db","illuminaHumanv1BeadID.db",
                "illuminaHumanv2BeadID.db","illuminaHumanv3BeadID.db","IRanges","limma","maSigPro",
                "MergeMaid","metaArray","MiPP","mogene10sttranscriptcluster.db","multtest",
                "org.Hs.eg.db","org.Mm.eg.db","org.Rn.eg.db","pamr","pdmclass","preprocessCore","R2HTML",
                "ragene10sttranscriptcluster.db","RankProd","RColorBrewer","Rgraphviz","rtracklayer","siggenes",
                "sizepower","ssize","tkrplot","tkWidgets","widgetTools","xtable", "HuExExonProbesetLocationHg19",
                "MoExExonProbesetLocation",  "RaExExonProbesetLocation", "edgeR", "baySeq", "girafe", "ChIPpeakAnno", "chipseq",  
                "BSgenome",  "snow", "RmiR", "RmiR.Hs.miRNA", "oneChannelGUI"))
\end{Sinput}
\end{Schunk}

oneChannelGUI inherits the core graphical interface of affylmGUI. This interface 
need, under windows, the installation of TCL/TK libraries that can be download from:
\url{http://www.activestate.com/Products/ActiveTcl/}

To load Hs/Mm/Rn exon 1.0 ST Affymtrix arrays users need to install
APT tools 1.12.0. The windows binaries can be downloaded from:
\url{http://www.affymetrix.com/support/developer/powertools/index.affx}
In addition library files for gene/exon arrays are directly downloaded and installed locally 
from oneChannelGUI interface, the first time an Exon 1.0 ST or Gene 1.0 ST analysis is started.
Or using the function \textit{oneChannelGUI: Set library folder and install Affy gene/Exon library files}
present in the General tools Menu.

\begin{Schunk}
\begin{Sinput}
IMPORTANT APT TOOLS AND EXON LIBRARY FILES NEED TO BE LOCATED 
IN A FOLDER CHARACTERIZED BY A PATH WITHOUT SPACES
C:/apt.1.8.0 THIS IS OK
C:/PROGRAM FILES/APT.1.8.0  STARTING APT TOOLS FROM oneChannelGUI will produce an error.
\end{Sinput}
\end{Schunk}


If you are interested to run RNA-seq secondary analysis it is also required the installation of perl.
The easy way is to install the active perl: \url{http://www.activestate.com/activeperl}

\subsection{Unix users}
The packages to be downloaded for unix users are those indicated for windows users unless for the 
TCL/TK libraries.

To use Tcl/Tk then the interface package tcltk must be installed into R.
If an R package uses Tcl/Tk then Tcl/Tk must be installed on the OS before the R 
package can be installed into R. 
Furthermore, these two Tcl/Tk packages are needed by oneChanneGUI, affylmGUI and limmaGUI for their 
functionality:
\begin{enumerate}
  \item BWidget, this is a package written entirely in the tcl scripting language and hence is not compiled. Consequently it is the same on any 
        platform and should be in the Tcl/Tk path. 
  \item Tktable, this package has some code written in C and hence is a compiled package. It therefore 
        is different for each type of CPU and OS.
\end{enumerate}

It is possible to encounter problems in installing those libraries on x64 machines.
For this reason I found quite useful the suggestions
of  Keith Satterley (24 Apr 2007) subject: Re: [Bioc-devel] Tcl/TK pckage "Bwidget"
available on the Bioconductor mailing list. 


\end{document}