\documentclass{article}\usepackage[]{graphicx}\usepackage[]{color} % maxwidth is the original width if it is less than linewidth % otherwise use linewidth (to make sure the graphics do not exceed the margin) \makeatletter \def\maxwidth{ % \ifdim\Gin@nat@width>\linewidth \linewidth \else \Gin@nat@width \fi } \makeatother

\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345} \newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}% \newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}% \newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}% \newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}% \newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}% \newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}% \newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}% \newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}% \newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}% \let\hlipl\hlkwb

\usepackage{framed} \makeatletter \newenvironment{kframe}{% \def\at@end@of@kframe{}% \ifinner\ifhmode% \def\at@end@of@kframe{\end{minipage}}% \begin{minipage}{\columnwidth}% \fi\fi% \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep \colorbox{shadecolor}{##1}\hskip-\fboxsep % There is no \@totalrightmargin, so: \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}% \MakeFramed {\advance\hsize-\width \@totalleftmargin\z@ \linewidth\hsize \@setminipage}}% {\par\unskip\endMakeFramed% \at@end@of@kframe} \makeatother

\definecolor{shadecolor}{rgb}{.97, .97, .97} \definecolor{messagecolor}{rgb}{0, 0, 0} \definecolor{warningcolor}{rgb}{1, 0, 1} \definecolor{errorcolor}{rgb}{1, 0, 0} \newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX

\usepackage{alltt} \input{../../LaTeX/package_style.tex} \title{GSE32323} \author{Angela Riffo-Campos \and Guillermo Ayala} \IfFileExists{upquote.sty}{\usepackage{upquote}}{} \begin{document} \maketitle \tableofcontents

\section{Data} The GSE32323 dataset was published by Khamas et al in 2012 (PMID: 22399497). The dataset include 17 colorectal cancer patients with samples from cancer and non-cancerous tissues and 10 samples from CRC cell lines. The cell lines samples were excluded in this analysis. \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{pacman}\hlopt{::}\hlkwd{p_load}\hlstd{(GEOquery,affy,arrayQualityMetrics)} \hlkwd{library}\hlstd{(org.Hs.eg.db)} \hlkwd{library}\hlstd{(hgu133plus2.db)} \hlkwd{library}\hlstd{(hgu133plus2cdf)} \hlkwd{library}\hlstd{(arrayQualityMetrics)} \hlkwd{library}\hlstd{(geneplotter)} \end{alltt} \end{kframe} \end{knitrout} Download the data. \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{GSE32323_RAW} \hlkwb{=} \hlkwd{getGEOSuppFiles}\hlstd{(}\hlstr{“GSE32323”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout} \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlkwd{setwd}\hlstd{(}\hlstr{“GSE32323/”}\hlstd{)} \hlkwd{system}\hlstd{(}\hlstr{“tar xvf GSE32323_RAW.tar”}\hlstd{)} \hlkwd{system}\hlstd{(}\hlstr{“rm GSE32323_RAW.tar”}\hlstd{)} \hlstd{GSE32323raw} \hlkwb{=} \hlkwd{ReadAffy}\hlstd{()} \hlstd{GSE32323raw} \hlkwd{dim}\hlstd{(}\hlkwd{exprs}\hlstd{(GSE32323raw))} \hlkwd{setwd}\hlstd{(}\hlstr{“../”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout} Quality controls. \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlkwd{table}\hlstd{(}\hlkwd{probes}\hlstd{(GSE32323raw,}\hlstr{“pm”}\hlstd{)} \hlopt{>=} \hlkwd{probes}\hlstd{(GSE32323raw,}\hlstr{“mm”}\hlstd{))} \hlstd{affy}\hlopt{::}\hlkwd{hist}\hlstd{(GSE32323raw)} \hlstd{affy}\hlopt{::}\hlkwd{boxplot}\hlstd{(GSE32323raw)} \hlkwd{arrayQualityMetrics}\hlstd{(}\hlkwc{expressionset} \hlstd{= GSE32323raw,} \hlkwc{do.logtransform} \hlstd{=} \hlnum{FALSE}\hlstd{)} \hlcom{## Transform to log2} \end{alltt} \end{kframe} \end{knitrout} \section{Normalization with RMA} \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{GSE32323} \hlkwb{=} \hlstd{affy}\hlopt{::}\hlkwd{rma}\hlstd{(GSE32323raw)} \hlkwd{dim}\hlstd{(GSE32323)} \hlkwd{class}\hlstd{(GSE32323)} \end{alltt} \end{kframe} \end{knitrout} The metadata or phenotypic variable is a text file included in the package. \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{file.path} \hlkwb{=} \hlkwd{system.file}\hlstd{(}\hlstr{“extdata”}\hlstd{,} \hlstr{“GSE32323_pData.csv”}\hlstd{,} \hlkwc{package}\hlstd{=}\hlstr{“tamidata3”}\hlstd{)} \hlkwd{read.csv}\hlstd{(file.path)} \hlkwd{pData}\hlstd{(GSE32323)} \hlkwb{=} \hlkwd{read.csv}\hlstd{(}\hlstr{“GSE32323_pData.csv”}\hlstd{)} \hlkwd{save}\hlstd{(GSE32323,}\hlkwc{file}\hlstd{=}\hlstr{“GSE32323.rda”}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout}

\end{document}