%\VignetteIndexEntry{CQN (Conditional Quantile Normalization)}
%\VignetteDepends{cqn}
%\VignetteDepends{scales}
%\VignettePackage{cqn}
\documentclass[12pt]{article}
<<echo=FALSE>>=
options(width=70)
@ 
\SweaveOpts{eps=FALSE,echo=TRUE,png=TRUE,pdf=FALSE,figs.only=TRUE}
\usepackage{fullpage}
\usepackage{times}
\usepackage[colorlinks=TRUE,urlcolor=blue,citecolor=blue]{hyperref}

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}
\newcommand{\Rmethod}[1]{{\texttt{#1}}}
\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
\newcommand{\Rclass}[1]{{\textit{#1}}}
\newcommand{\Rcode}[1]{{\texttt{#1}}}
\newcommand{\software}[1]{\textsf{#1}}
\newcommand{\R}{\software{R}}

\title{CQN (Conditional Quantile Normalization)}
\author{Kasper Daniel Hansen \\ \texttt{khansen@jhsph.edu}
\and
Zhijin Wu \\ \texttt{zhijin\_wu@brown.edu}}
\date{Modified: June 4, 2011.  Compiled: \today}
\begin{document}
\setlength{\parskip}{0.2\baselineskip}
\setlength{\parindent}{0pt}
\setkeys{Gin}{width=\textwidth}
\maketitle

\section*{Introduction}

This package contains the CQN (conditional quantile normalization)
method for normalizing RNA-seq datasets.  This method is described in
\cite{preprint}.

<<load,results=hide>>=
library(cqn)
library(scales)
@ 

\section*{Data}

As an example we use ten samples from Montgomery \cite{Montgomery}.
The data has been processed as described in \cite{preprint}.  First we
have the region by sample count matrix

<<data1>>=
data(montgomery.subset)
dim(montgomery.subset)
montgomery.subset[1:4,1:4]
colnames(montgomery.subset)
@ 

Because of (disc) space issues, We have removed all genes that have
zero counts in all 10 samples.  Next we have the \emph{sizeFactors}
which simply tells us how deep each sample was sequenced:

<<data2>>=
data(sizeFactors.subset)
sizeFactors.subset[1:4]
@ 

Finally, we have a matrix containing length and GC-content for each
gene.

<<data3>>=
data(uCovar)
head(uCovar)
@ 

Note that the row ordering of the count matrix is the same as the
row ordering of the matrix containing length and GC-content and that
the sizeFactor vector has the same column order as the count matrix.
We can formally check this

<<checkdata>>=
stopifnot(all(rownames(montgomery.subset) == rownames(uCovar)))
stopifnot(colnames(montgomery.subset) == names(sizeFactors.subset))
@ 

\section*{Normalization}

The methodology is described in \cite{preprint}.  The main workhorse is
the function \Rfunction{cqn} which fits the following model
\begin{displaymath}
  \log_2(\textrm{RPM}) = s(x) + s(\log_2(\textrm{length}))
\end{displaymath}
where $x$ is some covariate, $s$ are smooth functions (specifically
natural cubic splines with 5 knots), and $\textrm{RPM}$ are ``reads
per millions''.  We also have the function \Rfunction{cqn.fixedlength}
which fits the model
\begin{displaymath}
\log_2(\textrm{RPKM}) = s(x)
\end{displaymath}
In this model gene length is included as a known offset.

The basic call to \Rfunction{cqn} is relatively easy, we need the count
matrix, a vector of lengths, a vector of GC content and a vector of
sizeFactors.  Make sure that they all have the same ordering.

<<cqncall>>=
cqn.subset <- cqn(montgomery.subset, lengths = uCovar$length, 
                  x = uCovar$gccontent, sizeFactors = sizeFactors.subset,
                  verbose = TRUE)
cqn.subset
@ 

This normalized matrix is similar, but not equivalent, to the data
examined in \cite{preprint}.  The main differences are (1) in
\cite{preprint} we normalize 60 samples together, not 10 and (2) we
have removed all genes with zero counts in all 10 samples.

We can examine plots of systematic effects by using \Rfunction{cqnplot}.
The \Rfunarg{n} argument refers to the systematic effect, \Rfunarg{n=1} is
always the covariate specified by the \Rfunarg{x} argument above, while
\Rfunarg{n=2} is lengths.

<<cqnplot1,fig=TRUE,width=8,height=4>>=
par(mfrow=c(1,2))
cqnplot(cqn.subset, n = 1, xlab = "GC content", lty = 1, ylim = c(1,7))
cqnplot(cqn.subset, n = 2, xlab = "length", lty = 1, ylim = c(1,7))
@ 

The normalized expression values are
<<normalizedvalues>>=
RPKM.cqn <- cqn.subset$y + cqn.subset$offset
RPKM.cqn[1:4,1:4]
@ 
These values are on the $\log_2$-scale.

We can do a MA plot of these fold changes, and compare it to fold
changes based on standard RPKM.  First we compute the standard RPKM
(on a $\log_2$ scale):
<<rpkmvalues>>=
RPM <- sweep(log2(montgomery.subset + 1), 2, log2(sizeFactors.subset/10^6))
RPKM.std <- sweep(RPM, 1, log2(uCovar$length / 10^3))
@ 

We now look at differential expression between two groups of samples.
We use the same grouping as in \cite{preprint}, namely
<<groups>>=
grp1 <- c("NA06985", "NA06994", "NA07037", "NA10847", "NA11920")
grp2 <- c("NA11918", "NA11931", "NA12003", "NA12006", "NA12287")
@ 

We now do an MA-plot, but we only choose to plot genes with average standard
$\log_2$-RPKM of $\log_2(5)$ or greater, and we also form the M and A values:

<<whGenes>>=
whGenes <- which(rowMeans(RPKM.std) >= 2 & uCovar$length >= 100)
M.std <- rowMeans(RPKM.std[whGenes, grp1]) - rowMeans(RPKM.std[whGenes, grp2])
A.std <- rowMeans(RPKM.std[whGenes,])
M.cqn <- rowMeans(RPKM.cqn[whGenes, grp1]) - rowMeans(RPKM.cqn[whGenes, grp2])
A.cqn <- rowMeans(RPKM.cqn[whGenes,])
@ 

Now we do the MA plots, with alpha-blending

<<maplots,fig=TRUE,width=8,height=4>>=
par(mfrow = c(1,2))
plot(A.std, M.std, cex = 0.5, pch = 16, xlab = "A", ylab = "M", 
     main = "Standard RPKM", ylim = c(-4,4), xlim = c(0,12), 
     col = alpha("black", 0.25))
plot(A.cqn, M.cqn, cex = 0.5, pch = 16, xlab = "A", ylab = "M", 
     main = "CQN normalized RPKM", ylim = c(-4,4), xlim = c(0,12), 
     col = alpha("black", 0.25))
@ 

We can also color the genes according to whether they have high/low
GC-content.  Here one needs to be careful, because of overplotting.
One solution is to leave out all genes with intermediate GC content.
We define high/low GC content as the 10\% most extreme genes:

<<gcmaplots,fig=TRUE,width=8,height=4>>=
par(mfrow = c(1,2))
gccontent <- uCovar$gccontent[whGenes]
whHigh <- which(gccontent > quantile(gccontent, 0.9))
whLow <- which(gccontent < quantile(gccontent, 0.1))
plot(A.std[whHigh], M.std[whHigh], cex = 0.2, pch = 16, xlab = "A", ylab = "M", 
     main = "Standard RPKM", ylim = c(-4,4), xlim = c(0,12), 
     col = "red")
points(A.cqn[whLow], M.cqn[whLow], cex = 0.2, pch = 16, col = "blue")
plot(A.cqn[whHigh], M.cqn[whHigh], cex = 0.2, pch = 16, xlab = "A", ylab = "M", 
     main = "CQN normalized RPKM", ylim = c(-4,4), xlim = c(0,12), 
     col = "red")
points(A.cqn[whLow], M.cqn[whLow], cex = 0.2, pch = 16, col = "blue")
@

Note that genes/regions with very small counts should not be relied
upon, even if the CQN normalized fold change are big.  They should be
filtered out using some kind of statistical test, good packages for
this are \Rpackage{DESeq}\cite{DESeq} and
\Rpackage{edgeR}\cite{edgeR}.

\section*{Import into edgeR}

First we construct a \Robject{DGEList}.  In the \Rfunarg{groups}
argument we use that the first 5 samples (columns) in
\Robject{montgomery.subset} is what we earlier called \Robject{grp1}
and the last 5 samples (columns) are \Robject{grp2}.

<<edgeRconstructor>>=
library(edgeR)
d.mont <- DGEList(counts = montgomery.subset, lib.size = sizeFactors.subset, 
                  group = rep(c("grp1", "grp2"), each = 5), genes = uCovar)
@ 

In this object we cannot (unfortunately, yet) also store the computed
offsets.  Since we will use the offsets computed by \Rpackage{cqn},
there is no need to normalize using the normalization tools from
\Rpackage{edgeR}, such as \Rfunction{calcNormFactors}.  Also, as is
clearly described in the \Rpackage{edgeR} user's guide, the
\Rfunarg{lib.size} is unnecessary, since we plan to use the offsets
computed from \Rpackage{cqn}.

Using \Rpackage{edgeR} is well described in the user's guide, and we
refer to that document for further information.  The analysis
presented below should be thought of as an example, and not
necessarily the best analysis of this data.

The first step is estimating the dispersion parameter(s).  Several
methods exists, such as \Rfunction{estimateGLMCommonDisp} or
\Rfunction{estimateTagwiseDisp}.  We also need to setup a design
matrix, which is particular simple for this two group comparison.
Further information about constructing design matrices may be found in
both the \Rpackage{edgeR} user's guide and the \Rpackage{limma} user's
guide. 

<<edgeRdisp>>=
design <- model.matrix(~ d.mont$sample$group)
d.mont.cqn <- estimateGLMCommonDisp(d.mont, design = design, offset = cqn.subset$offset)
@ 

After fitting the dispersion parameter(s), we need to fit the model,
and do a test for significance of the parameter of interest.  With
this design matrix, there are two coefficients.  The first coefficient
is just an intercept (overall level of expression for the gene) and it
is (usually) not meaningful to test for this effect.  Instead, the
interesting coefficient is the second one that encodes a group difference.

<<edgeRfit>>=
efit.cqn <- glmFit(d.mont.cqn, design = design, offset = cqn.subset$offset)
elrt.cqn <- glmLRT(d.mont.cqn, efit.cqn, coef = 2)
topTags(elrt.cqn, n = 2)
@ 

\Rfunction{topTags} shows (per default) the "top 10" genes.  In this
case, since we have biological replicates and just a random group
structure, we would expect no differentially expression genes.
Instead we get

<<>>=
summary(decideTestsDGE(elrt.cqn))
@ 

significantly differentially expressed at an FDR (false discovery
rate) of 5\%.  We may contrast this with the result of not using
\Rpackage{cqn}: 

<<edgeRstd>>=
d.mont.std <- estimateGLMCommonDisp(d.mont, design = design)
efit.std <- glmFit(d.mont.std, design = design)
elrt.std <- glmLRT(d.mont.std, efit.std, coef = 2)
summary(decideTestsDGE(elrt.std))
@ 

What is arguably as important is that we achieve a much better
estimation of the fold change using \Rpackage{cqn}.

\section*{SessionInfo}

<<sessionInfo,results=tex,echo=FALSE>>=
toLatex(sessionInfo())
@ 

\begin{thebibliography}{4}
\bibitem{preprint} Hansen, K.D., Irizarry, R.A., and Wu, W.  Removing
    technical variability in RNA-seq data using conditional quantile
    normalization. \emph{Johns Hopkins, Dept of Biostatistics
      Working Papers}, Working Paper 227 (2011). url:
    \url{http://www.bepress.com/jhubiostat/paper227} 
  \bibitem{Montgomery} Montgomery, S.B. \emph{et al.}  Transcriptome
    genetics using second generation sequencing in a Caucasian
    population. \emph{Nature} \textbf{464}, 773--777.  doi:
    \href{http://dx.doi.org/10.1038/nature08903}
    {\path{10.1038/nature08903}}
  \bibitem{DESeq} Anders, S. and Huber, W. Differential expression
    analysis for sequence count data.  \emph{Genome Biology}
    \textbf{11}(10), R106 (2010).  doi:
    \href{http://dx.doi.org/10.1186/gb-2010-11-10-r106}{\path{10.1186/gb-2010-11-10-r106}}
  \bibitem{edgeR} Robinson, M.D., McCarthy, D.J., Smyth, G.K.  edgeR:
    a Bioconductor package for differential expression analysis of
    digital gene expression data.  \emph{Bioinformatics}
    \textbf{26}(1), 139--140 (2010).  doi:
    \href{http://dx.doi.org/10.1093/bioinformatics/btp616}{\path{10.1093/bioinformatics/btp616}}
  \end{thebibliography}
\end{document}

% Local Variables:
% LocalWords: LocalWords quantile sizeFactors datasets GC covariate
% LocalWords: CQN cqn cqnplot RPKM overplotting cqn.fixedlength calcNormFactors
% End:

