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%\VignetteKeywords{one channel microarray,extended Affymetrix GUI, limma, quality control, data filtering, time course, alternative splicing}
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\begin{document}
\title{oneChannelGUI Package: What is new}
\author{Raffaele A Calogero, Francesca Cordero, Remo Sanges}
\date{May 03, 2010}
\maketitle

\section{oneChannelGUI Reference}
\begin{Schunk}
\begin{Sinput}
oneChannelGUI: a graphical interface to Bioconductor tools, 
designed for life scientists who are not 
familiar with R language.
Sanges R, Cordero F, Calogero RA.
Bioinformatics. 2007 Dec 15;23, 24, 3406-8.
\end{Sinput}
\end{Schunk}

\section{Updates}
\subsection{1.8.8} 
Bioconductor BeadStudion V3: report generated by BeadStudio V3 can be loaded in oneChannelGUI.
BeadStudio V3 report MUST be a SAMPLE PROBE PROFILE containing at least 
\begin{Schunk}
\begin{Sinput}
AVG_Signal
\end{Sinput}
\end{Schunk}
\subsection{1.8.9} 
Fast parameter in GCRMA is set to FALSE.
\subsection{1.10.7}
Revised annotation for variant exons has been added. After statistical detection of putative splicing.
It is now possible to select only exon-level probesets associated to non-costitutive exons, i.e. those 
exons associated only to a to a subset of isoforms.
\subsection{1.10.8}
Added Cosie method to correct SI index: Gaidatzis et al. Nucleic Acids Research, 2009, pg. 1.
Since intcor function from metaArray package has a bug it was sobstituted by intCor from MergeMaid package.
Alternative splicing events can be visualized on the UCSC Genome Browser via rtracklayer.
\subsection{1.10.9}
Starting from the work of Shah and Pallas work BMC Bioinformatics. 2009 Jan 20;10:26. Limma routines available for
gene-level analysis were implemented at exon-level to detect alternative splicing events.
\subsection{1.11.17}
Using Bioconductor hugene10stprobeset.db, mogene10stprobeset.db and ragene10stprobeset.db for GENE 1.0 ST arrays
istrad of the internal annotaiton based on Affymetrix data.
\subsection{1.13.4}
Exon-level annotation is provided by three external packages: HuExExonProbesetLocationHg19, MoExExonProbesetLocation, RaExExonProbesetLocation.
oneChannelGUI is now providing a basic interface to the secondary analysis of Next Generation Sequencing data. The inteface is designed for
ncRNAs quantification analysis. 
\subsection{1.15.1}
Two groups linear model analysis with batch effect was added.
\end{document}



