% \VignetteIndexEntry{RPA}
%The above line is needed to remove a warning in R CMD check
\documentclass[12pt]{article}

\usepackage{amsmath,amssymb,amsfonts}
\usepackage{hyperref}
%\usepackage[authoryear,round]{natbib}
\usepackage{Sweave}

\textwidth=6.2in
\textheight=8.5in
\oddsidemargin=.1in
\evensidemargin=.1in
\headheight=-.3in

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}

\def\muj{\mathbf{\mu}_j}
\def\mujs{\{\mathbf{\mu}_j\}}

\def\s{\{\mathbf{s}\}}
\def\st{\mathbf{s}^t}
\def\sj{\mathbf{s}_j}
\def\sij{s_{ij}}
\def\sjs{\mathbf{s}_{j=1}^J}
\def\sjt{\mathbf{s}_j^t}
\def\stj{s_{tj}}
\def\scj{s_{cj}}
\def\stjs{\{s_{tj}\}_t}
\def\sjI{\mathbf{s}_j^1}
\def\sjT{\mathbf{s}_j^T}

\def\m{\mathbf{m}}
\def\mj{\mathbf{m}_j}
\def\mjs{\{\mathbf{m}_j\}}
\def\mtj{m_{tj}}

\def\gj{\{\mathbf{g}_j\}}
\def\gi{g_i}
\def\gt{g_t}
\def\gc{g_c}
\def\g{\mathbf{g}}

\def\d{\mathbf{d}}
\def\dt{d_t}
\def\djt{\mathbf{d}_j^t}
\def\djr{\mathbf{s}_{j}}

\def\TauSq{\boldsymbol{\tau}^2}
\def\tauj{\mathbf{\tau}_j}
\def\taus{\{\tau_j^2\}}
\def\taujSq{\mathbf{\tau}_j^2}
\def\tauOneSq{\mathbf{\tau}_1^2}
\def\tauPSq{\mathbf{\tau}_J^2}

\def\epsilonj{\varepsilon_j}
\def\epsilonij{\mathbf{\varepsilon}_{ij}}
\def\epsiloncj{\varepsilon_{cj}}
\def\epsilontj{\varepsilon_{tj}}
\def\epsilontjs{\{\varepsilon_{tj}\}_t}
\def\epsiloncjs{\{\varepsilon_{cj}\}_j}
\def\Epsilonj{\boldsymbol{\varepsilon}_j}
\def\Epsiloncj{\boldsymbol{\varepsilon}_{cj}}

\def\alphaj{\alpha_j}
\def\betaj{\beta_j}
\def\alphahatj{\hat{\alpha}_j}
\def\betahatj{\hat{\beta}_j}

\def\zi{z_i}
\def\j{\mathbf{j}}
\def\sigmaj{\sigma_j}
\def\lambdaj{\lambda_j}

\author{Leo Lahti\footnote{http://www.iki.fi/Leo.Lahti}\\University of Helsinki\\leo.lahti@iki.fi}
  
\begin{document} \title{Robust Probabilistic Averaging (RPA)}

\maketitle 

\section{Introduction}
 
\Rpackage{RPA} (Robust Probabilistic
Averaging)\footnote{\url{http://bioconductor.org/packages/release/bioc/html/RPA.html}}
is a fully scalable preprocessing method for arbitrarily large short
oligonucleotide microarray atlases. It outperforms the standard RMA
model \cite{Irizarry03rma} on moderately sized data sets
\cite{Lahti11, Lahti12} and unlike the another scalable alternative,
fRMA \cite{McCall2011}, it is applicable to all short oligonucleotide
platforms. RPA can be additionally used for probe reliability
analysis, and for general summarization of normally distributed
multivariate observations that target the same object with varying
degrees of noise and bias.


\section{Usage examples}

For usage examples on-line, see https://github.com/antagomir/RPA/wiki


\section{Methodology and Citations}

For details, see \cite{Lahti11, Lahti12}. Kindly cite these documents if you find the method useful.


\section{Details}

This document was written using:

<<details>>=
sessionInfo()
@

%\bibliographystyle{abbrv}
%\bibliography{RPA}

\begin{thebibliography}{10}

\bibitem{Irizarry03rma}
R.~A. Irizarry, B.~M. Bolstad, F.~Collin, L.~M. Cope, B.~Hobbs, and T.~P.
  Speed.
\newblock {Summaries of Affymetrix GeneChip probe level data}.
\newblock {\em Nucl. Acids Res.}, 31(4):e15, 2003.

\bibitem{Lahti11}
L.~Lahti, L.~L. Elo, T.~Aittokallio, and S.~Kaski.
\newblock Probabilistic analysis of probe reliability in differential gene
  expression studies with short oligonucleotide arrays.
\newblock {\em {IEEE/ACM Transactions on Computational Biology and
  Bioinformatics}}, 8(1):217--225, 2011.

\bibitem{Lahti12}
L.~Lahti, A. Torrente, L.~L. Elo, A. Brazma, J. Rung.
\newblock A fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases
\newblock {\it Nucl. Acids Res.} 2013. In press. Preprint available at http://arxiv.org/abs/1212.5932

\bibitem{McCall2011}
MN McCall and RA Irizarry.
\newblock Thawing Frozen Robust Multi-array Analysis (fRMA)
\newblock {\em BMC Bioinformatics} 12:369, 2011.

\end{thebibliography}


\end{document}