% \VignetteIndexEntry{PCOT2 Vignette}
% \VignetteDepends{pcot2}
% \VignetteKeywords{Correlation Analysis}
% \VignettePackage{pcot2}



\documentclass[a4paper]{article}

\title{PCOT2: Principal Coordinates and
  Hotelling's $T^2$ for the analysis of microarray data}

\author{Sarah Song and Mik Black}

\begin{document}

\maketitle 
\section{Overview}
\texttt{pcot2} is an R-package for the analysis of groups of genes in
microarray experiments. It utilizes inter-gene correlation information
to detect significant alterations in the activities of gene
sets. Incorporating additional (usually functional) information into
the data analysis process allows gene interactions to be investigated
in a statistical framework. One of the reasons that gene set analysis
is becoming important is that it is suitable for detecting small
coordinated changes in expression of groups of genes which are
functionally related, which may not be considered significant in a
single gene analysis. This vignette gives a tutorial-style
introduction to the functions in the \texttt{pcot2} package. These
functions are used for testing and visualizing changes in expression
activity for groups of genes. 

\section{Example: ALL/AML data}
In this example the ALL/AML leukemia data set of Golub \textit{et al.}(1999) is
used to illustrate the functionality of the \texttt{pcot2}
package. This data set contains 38 bone marrow samples obtained from
adult leukemia patients, 11 relating to acute myeloid leukemia (AML,
class 1) and 27 relating to acute lymphoblastic leukemia (ALL, class
0). Gene expression levels were measured using Affymetrix high density
oligonucleotide arrays containing 6817 human genes, of which 3051
genes were considered suitable for analysis by Golub et al.(1999)
after pre-processing. This data set is available as part of the
\texttt{multtest} package and gene sets are defined as KEGG pathways
using the \texttt{hu6800} annotation package. Both packages can be
downloaded from www.bioconductor.org.  
<<>>=
library(pcot2)
library(multtest)
library(hu6800)  
set.seed(1234567)
@

\section{The \texttt{pcot2} function}
The \texttt{pcot2} function implements the PCOT2 testing method, which
is a two-stage permutation-based approach for testing changes in
activity in pre-specified gene sets. The function requires at least
three inputs: gene expression data, sample class labels, and a gene
category indicator matrix. The gene expression data should be in the
form of a matrix with no missing values. Data pre-processing
(e.g. normalization) must therefore take place before running the
PCOT2 analysis.  

<<>>=
data(golub)
rownames(golub) <- golub.gnames[,3]
colnames(golub) <- golub.cl
@

The class labels represent two distinct experimental conditions (e.g.,
AML and ALL). 

<<>>=
golub.cl
@

\noindent
The gene category indicator matrix is designed to indicate presence or
absence of genes in the pre-defined gene categories (e.g., gene
pathways). The indicator matrix contains rows representing gene
identifiers for genes present in the expression data, and columns
representing pre-defined group names. The values 1 or 0 indicate the
presence or absence of a gene in a particular group. 

In this example, the \texttt{hu6800} annotation package is used to
define the KEGG (http://www.genome.jp/kegg/pathway.html) pathways for
all of 3051 genes in the data. The \texttt{getImat} function is used
to generate an indicator matrix which includes 65 KEGG pathways
containing at least 10 of the total 3051 genes. 

<<>>=
KEGG.list <- as.list(hu6800PATH)
imat <- getImat(golub, KEGG.list, ms=10) 
colnames(imat) <- paste("KEGG", colnames(imat), sep="")
dim(imat)
@

Permutations are used to produce $p$-values based on the null
distribution of the $T^2$ statistic.  By default \texttt{pcot2} will
automatically run 1000 permutations. In order to minimize the time
taken to build this vignette, only 10 permutations have been performed.

<<>>=
results <- pcot2(golub, golub.cl, imat, iter=10)
@

The output from the \texttt{pcot2} function can contain information on
either all pathways or just significantly differentially expressed
pathways, based on the value of $\alpha$ used in the function, where
$\alpha$ determines the significance threshold for the permutation
$p$-values. For each KEGG pathway, the number of genes in the pathway
is listed, along with Hotelling's $T^2$ statistic. These are followed
by parametric $p$-values for the test statistic, both raw and
adjusted. The last two columns provide raw and adjusted
permutation-based $p$-values. The default adjustment method is the false
discovery rate controlling method of Benjamini and Yekutieli (2001). 

<<>>=
results$res.sig
results$res.all
@

In the {\tt pcot2} function, the $T^2$ statistic can be calculated in
two ways, using either a pooled estimate of correlation for the two
classes (default) or an unpooled estimate. And users can set \textit{var.equal=F} if the correlation
structure is assumed to differ across the two classes.

In the first step of the PCOT2 analysis, the dimensionality of the gene
expression data is reduced via principal coordinates. The default
dimensionality in the \texttt{pcot2} function is set as
\textit{ncomp=2}.  In the second step of the PCOT2 analysis, the distances between the 
transformed groups are calculated via euclidean distances by
default. Other distances (e.g., correlation or Spearman distances)
can also be used by defining \textit{dist.method} in the function. 
A permutation $p$-value for each category is calculated by
re-arranging the sample labels.  The permutations can also be
performed by permuting rows (genes), using {\tt permu='ByRow'}.  

Table 1 lists computation times (in minutes) required to run 1000
permutations of the \texttt{pcot2}
function on the AML/ALL data under various parameter
configurations.  The two machines used were a 3.2GHz Pentium 4 with 1Gb
RAM running Microsoft Windows XP and R 2.1.0 (PC), and a 1.70GHz
Pentium M with 256Mb of RAM running Fedora Core 3 and R 2.2.0 (Unix).

\begin{table}[!hh]
\caption {\textit{Computation times (minutes, 1000 permutations)}}
\begin{tabular}{l c c}
\hline
Changes  & PC machine & UNIX machine\\
\hline
default setting & 5.6 & 6.8 \\ 
var.equal=F & 5.5 & 6.8 \\ 
comp=8 & 6 & 7.6 \\
dist.method="euclidean" & 4.8 & 6 \\
permu="ByRow" & 5.6 & 6.8 \\
\hline
\end{tabular}
\end{table}



\section{The \texttt{corplot} and \texttt{corplot2} functions}
The \texttt{corplot} and \texttt{corplot2} functions enable
visualization of both correlation and gene expression information for
a particular gene category, in particular the groups identified as
being differentially expressed.  The plot
produced by the \texttt{corplot} function displays the pooled correlation
calculated from the two classes, while the \texttt{corplot2} function
produces a plot based on unpooled correlation. Gene names can
be added to the plot using \textit{add.name=T} (default). The
font size can be changed by setting the \textit{font.size}
argument. The \textit{main} option specifies the title of the plot. 

<<>>=
sel <- c("04620","04120")
pvalue <- c(0.001, 0.72)
library(KEGG)
pname <- unlist(mget(sel, env=KEGGPATHID2NAME))
main <- paste("KEGG", sel, ": ", pname, ": ", "P=", pvalue, sep="")
for(i in 1:length(sel)){
fname <- paste("corplot2-KEGG",sel[i] , ".jpg", sep="")
jpeg(fname, width=1600, height=1200, quality=100)
selgene <- rownames(imat)[imat[,match(paste("KEGG",sel,sep="")[i],colnames(imat))]==1]
corplot2(golub, selgene, golub.cl, main=main[i])
dev.off()
}
@

\begin{figure}[!tpb]%figure1
\centerline{\includegraphics[scale=0.4,angle=0]{corplot2-KEGG04620.jpg}}
\caption{KEGG04620}\label{fig:01}
\end{figure}

\begin{figure}[!tpb]%figure2
\centerline{\includegraphics[scale=0.4,angle=0]{corplot2-KEGG04120.jpg}}
\caption{KEGG04120}\label{fig:02}
\end{figure}

%<<plot2, results=hide, fig=T>>=
%corplot2(golub, selgene, golub.cl, main=main[2])
%@

The argument \textit{inputP} allows users to input the $p$-values of
individual genes calculated using other approaches, such as the limma package 
(Smyth \textit{et al.}, 2004), allowing the results from both per-gene and 
per-pathway analysis to be printed on a single plot. To allow
users to identify genes from in correlation image plots, the 
argument \textit{gene.locator=T} allows the selection of interesting 
(e.g., highly correlated and differential
expressed between two classes) genes by clicking beginning and end
points on the main diagonal of the image plots.  This prints the
identifiers for the selected genes.  Further details of this
functionality are provided in the HowToUseGeneLocator.pdf document.
The usage of \texttt{corplot2} is similar to that for the \texttt{corplot}
function. 

%<<>>=
%selgene <- rownames(imat)[imat[,match("KEGG04620",colnames(imat))]==1]
%out <- corplot2(golub, selgene, golub.cl, main="KEGG04620", add.name=F, gene.locator=T)
%out
%@

\section{The \texttt{aveProbes} function}
In Affymetrix gene expression data, a unique gene can often link to multiple
probe sets, with such genes then having a greater influence on the
pathway analysis (particularly if the gene is differentially expressed). 
In order to solve this problem, the \texttt{aveProbe} function is
provided to change the multiple probe
data to the unique gene data by taking the median of the probe
values. This function can be used to transform both expression data and
the indicator matrix by providing a vector of unique gene identifiers. 

<<>>=
pathlist <- as.list(hu6800PATH)
pathlist <- pathlist[match(rownames(golub), names(pathlist))]
ids <- unlist(mget(names(pathlist), env=hu6800SYMBOL))
#### transform data matrix only ####
newdata <- aveProbe(x=golub, ids=ids)$newx
#### transform both data and imat ####
output <- aveProbe(x=golub, imat=imat, ids=ids)
newdata <- output$newx
newimat <- output$newimat
newimat <- newimat[,apply(newimat, 2, sum)>=10]
dim(newdata)
dim(newimat)
@


After the multiple probe data set has been changed to the unique gene symbol data, further analysis such as testing and visualizing pathways can be done on the new data set. 

%\begin{figure}[!tpb]%figure3
%\centerline{\includegraphics[scale=0.4,angle=0]{corplot2-ave-04620-small.jpg}}
%\caption{Averaging multiple probes on KEGG04620}\label{fig:03}
%\end{figure}

%<<>>=
%selgene <- rownames(newimat)[newimat[,match("KEGG04620",colnames(newimat))]==1]
%out <- corplot2(newdata, selgene, golub.cl, main="KEGG04620", add.name=F, gene.locator=T)
%out
%@


\begin{thebibliography}{}

\bibitem{ben-yek-2001} Benjamini,B.Y. and Yekutieli,D. (2001) The control of the false discovery rate in multiple testing under dependency. {\it The Annals of Statistics}, {\bf 29}, 1165-1188.

\bibitem{bioconductor04} Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. {\it et al.} (2004) Bioconductor: open software development for computational biology and bioinformatics. {\it Genome Biology}, {\bf 5}, R80.

\bibitem{golub-1999} Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gaasenbeek,M., Mesirov,J.P., Coller,H., Loh,M.L., Downing,J.R., Caligiuri,M.A. {\it et al.} (1999) Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring, {\it Science}, {\bf 286}, 531-537.

\bibitem{smyth-2004} Smyth,G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. {\it Statistical Applications in Genetics and Molecular Biology}, {\bf 3}, No.1, Article 3.

\end{thebibliography}

\end{document}

