\documentclass[12pt]{article}
\title{Notes for BioConductor: pre-process gene expression}
\author{Guiyuan Lei\footnote{E-mail: Guiyuan.Lei@ncl.ac.uk}}
\date{14 March, 2006}
\begin{document}
\maketitle
BioConductor is an open source and open development software project
for the analysis and comprehension of genomic data.
\section{Install of BioConductor}
The website of http://www.bioconductor.org/docs/install-howto.html describe how to install BioConductor. I choose to install it by biocLite.R\\
For me, in order to connect internet in linux terminal. I have to set http proxy by add\\
setenv http\_proxy ``http://wwwcache.ncl.ac.uk:8080''\\
into file .cshrc under my home directory.\\
Then follow the following steps:
\begin{enumerate}
\item Run R (the version should be higher than 2.1.0). I type ``/usr/bin/R'' because the R in my local linux is verions 2.0.1, the adiminstor did something so that I can use version 2.1.0 by typing this command. But something wrong with this. 
\item source("http://www.bioconductor.org/biocLite.R")
\item biocLite(lib=''/data/BioConductor'',destdir=''/dataBioConductor/downloaded'')\\
argument ``lib'' is the directory where the BioConductor will be installed, the argument ``destdir'' is for the directory where the install files/packages be downloaded, you can delete files under this directory after the installation is finished. \\
Error during installation: 
\end{enumerate}

 The version of R should be higher than 2.1.0. I type ``/usr/bin/R'' because the R in my local linux is verions 2.0.1, the adiminstor did something so that I can use version 2.1.0 by typing this command. But something wrong with this. After the installation, if I type \\
library(affy), R reported``Error in library(affy) : there is no package called 'affy'''. If I run R by typing\\
R\\
instead of\\
/usr/bin/R\\
When I use ``library(affy)'', I got a warning:\\
``warning: incorrect permissions to edit package database\\
/usr/local/R\_2.0.1/lib/library/liblisting.Rda''\\

 The argument ``lib'' in command biocLite() is the directory where the BioConductor will be installed, the argument ``destdir'' is for the directory where the install files/packages be downloaded, you can delete files under this directory after the installation is finished. \\

Error during installation: 
\begin{enumerate}
\item affyPLM not successfully installed
\item /usr/bin/ld: cannot find -lblas-3
\end{enumerate}

\section{Use BioConductor to deal with affymetrix microarray data}
\begin{enumerate}
\item Put all .CEL files in one directory, like /Huang
\item Run R under the directory /Huang
\item library(affy)
\item Read in data by typing ``Huang$<-$ ReadAffy()''
\item Do Normalization by typing ``eset$<-$justRMA()''
\item Save data, write.exprs(eset,file=''mydata.txt'')
\item Write to excel format, exprs2excel(eset,file=''mydata.CSV'')
\end{enumerate}

\section{Resources on BioConductor}
\begin{itemize}
\item Downloading All Packages From A Repository\\
To download all of the packages from a repository into a directory, use the download.packages2 function. To do this, select the repository you wish to download the packages from (using repositories for instance) and run download.packages2(repEntry=REP, destDir=DIR), where REP is your ReposEntry object and DIR is the directory you'd like them downloaded to (e.g. ".").\\
/data/cdfenvs/repos: A repository for the Bioconductor CDF data packages.
\item affyDemo: Introcudtion to Bioconductor affy Package\\
http://www-edlab.cs.umass.edu/cs691k/conlon/readings/affyDemo.pdf 
\item vignettes\\
http://www.bioconductor.org/docs/vignettes.html 
\end{itemize}

\section{To do}
\begin{enumerate}
\item Re-install BioConductor after 
  \begin{enumerate}
       \item Upgrade R to version 2.1.0
       \item Install blas
  \end{enumerate}
\item How to tell ReadAffy() which CDF file to be used for loaded .CEL fils?
\end{enumerate}
\end{document}

