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\author{Ben Bolstad}
\begin{document}
\title{affy: Built-in Processing Methods}
\maketitle
\tableofcontents
\section{Introduction}

This document describes the preprocessing methods that have currently
been built into the \verb+affy+ package.  Hopefully it will clarify
for the reader what each of the routines does. There is a separate
vignette which describes how you might write your own routines and use
them in combination with the built-in routines. 

As usual, loading the package in your \verb+R+ session is required. 
\begin{Sinput}
R> library(affy) ##load the affy package
\end{Sinput}
<<echo=F,results=hide>>=
library(affy)
@

\section{Background methods}

You can see the background correction methods that are built into the
package by examining the variable \verb+bgcorrect.method+. 

<<>>=
bgcorrect.methods()
@

\subsection{none}

Calling this method actually does nothing. It returns the object
unchanged. May be used as a placeholder. 

\subsection{rma/rma2}

These are background adjustment implementations for the rma method
\cite{iriz:etal:2003}. They differ only in how they estimate a set of
parameters (generally you should use \verb+rma+ in preference to
\verb+rma2+. In both cases PM probe intensities are corrected by using
a global model for the distribution of probe intensities. The model is
suggested by looking at plots of the empirical distribution of probe
intensities.  In particular the observed PM probes are modeled as the
sum of a normal noise component N (Normal with mean $\mu$ and variance
$\sigma^2$) and a exponential signal component S (exponential with
mean $\alpha$). To avoid any possibilty of negatives, the normal is
trucated at zero. Given we have O the observed intensity, this then
leads to an adjustment. 

\begin{equation*}
E\left(s \lvert O=o\right) = a + b \frac{\phi\left(\frac{a}{b}\right)
  - \phi\left(\frac{o-a}{b}\right)}{\Phi\left(\frac{a}{b}\right) +
  \Phi\left(\frac{o-a}{b}\right) - 1 } 
\end{equation*}
where $a =  s- \mu - \sigma^2\alpha$ and $b = \sigma$. Note that
$\phi$ and $\Phi$ are the standard normal distribution density and
distribution functions respectively. 

Note that MM probe intensitys are not corrrected by either of these routines.

\subsection{mas}

This is an implementation of the background correction method outlined
in the Statistical Algorithms Description Document
\cite{affy:tech:2002}. The chip is broken into a grid of 16
rectangular regions. For each region the lowest 2\% of probe
intensities are used to compute a background value for that grid. Each
probe is then adjusted based upon a weighted average of the
backgrounds for each of the regions. The weights are based on the
distances between the location of the probe and the centriods of 16
different regions. Note this method corrects both PM and MM probes. 

\section{Normalization Methods}

You can see the background correction methods that are built into the
package by examining the variable \verb+bgcorrect.method+. 
<<>>=
normalize.AffyBatch.methods()
@

The Quantile, Contrast and Loess normalizations have been discussed
and compared in \cite{bols:etal:2003}. 

\subsection{quantiles/quantiles.robust}

The quantile method was introduced by \cite{bols:etal:2003}. The goal
is to give each chip the same empirical distribution. To do this we
use the following algorithm where $X$ is a matrix of probe intensities
(probes by arrays):  

\begin{enumerate}
\item Given $n$ array of length $p$, form $X$  of dimension $p \times n$  where
each array is a column
\item Sort each column of $X$ to give $X_{\mbox{sort}}$
\item Take the means across rows of $X_{\mbox{sort}}$ and assign this mean to each element in the row to get $X'_{\mbox{sort}}$
\item Get $X_{\mbox{normalized}}$ by rearranging each column of $X'_{\mbox{sort}}$ to have the same ordering as original $X$
\end{enumerate}
 
The quantile normalization method is a specific case of the
transformation $x'_{i} = F^{-1}\left(G\left(x_{i}\right)\right)$,
where we estimate $G$ by the empirical distribution of each array and
$F$ using the empirical distribution of the averaged sample quantiles.
Quantile normalization is pretty fast. 

The {\tt quantiles} function performs the algorithm as above. The {\tt
  quantile.robust} function allows you to exclude or down-weight
arrays in the computation of $\hat G$ above. In most cases we have
found that the {\tt quantiles} method is sufficient for use and {\tt
  quantiles.robust} not required.   

\subsection{loess}

There is a discussion of this method in \cite{bols:etal:2003}. It
generalizes the $M$ vs $A$ methodology proposed in \cite{Dudoit:2002}
to multiple arrays. It works in a pairwise manner and is thus slow
when used with a large number of arrays. 

\subsection{contrasts}

This method was proposed by \cite{astr:2003}. It is also a variation
on the  $M$ vs $A$ methodology, but the normalization is done by
transforming the data to a set of contrasts, then normalizing. 

\subsection{constant}

A scaling normalization. This means that all the arrays are scaled so
that they have the same mean value. This would be typical of the
approach taken by Affymetrix. However, the Affymetrix normalization is
usually done after summarization (you can investigate
\verb+affy.scalevalue.exprSet+ if you are interested) and this
normalization is carried out before summarization. 

\subsection{invariantset}

A normalization similar to that used in the dChip software
\cite{li:wong:2001a}. Using a baseline array, arrays are normalized by
selecting invariant sets of genes (or probes) then using them to fit a
non-linear relationship between the ``treatment'' and ``baseline''
arrays. The non-linear relationship is used to carry out the
normalization. 

\subsection{qspline}

This method is documented in \cite{workman:etal:2002}. Using a target array (either one of the arrays or a synthetic target), arrays are normalized by fitting splines to the quantiles, then using the splines to perform the normalization.

\section{PM correct methods}

<<>>=
pmcorrect.methods()
@
\subsection{mas}

An {\it ideal mismatch} is subtracted from PM. The ideal mismatch is
documented by \cite{affy:tech:2002}. It has been designed so that you
subtract MM when possible (ie MM is less than PM) or something else
when it is not possible. The Ideal Mismatch will always be less than
the corresponding PM and thus we can safely subtract it without risk
of negative values.  

\subsection{pmonly}

Make no adjustment to the pm values.

\subsection{subtractmm}

Subtract MM from PM. This would be the approach taken in MAS 4
\cite{affy4}. It could also be used in conjuntion with the Li-Wong
model. 

\section{Summarization methods}

<<>>=
express.summary.stat.methods()
@

\subsection{avgdiff}

Compute the average. This is the approach that was taken in \cite{affy4}.

\subsection{liwong}

This is an implementation of the methods proposed in
\cite{li:wong:2001a} and \cite{li:wong:2001b}. The Li-Wong MBEI is
based upon fitting the following multi-chip model to each probeset 
\begin{equation}
y_{ij} = \phi_i \theta_j + \epsilon_{ij}
\end{equation}
where $y_{ij}$ is $PM_{ij}$ or the difference between
$PM_{ij}-MM_{ij}$. The $\phi_i$ parameter is a probe response
parameter and $\theta_j$ is the expression on array $j$. 


\subsection{mas}

As documented in \cite{affy:tech:2002}, a robust average using 1-step
Tukey biweight on $\log_2$ scale. 

\subsection{medianpolish}

This is the summarization used in the RMA expression summary
\cite{iriz:etal:2003}. A multichip linear model is fit to data from
each probeset. In particular for a probeset $k$ with $i=1,\dots,I_k$
probes and data from $j=1,\dots,J$ arrays we fit the following model 
\begin{equation*}
\log_2\left(PM^{(k)}_{ij}\right) = \alpha_i^{(k)} + \beta_j^{(k)} + \epsilon_{ij}^{(k)}
\end{equation*}
where $\alpha_i$ is a probe effect and $\beta_j$ is the $\log_2$
expression value. The medianpolish is an algorithm (see
\cite{tukey:1977}) for fitting this model robustly. Please note that
expression values you get using this summary measure will be in
$\log_2$ scale. 

\subsection{playerout}

This method is detailed in \cite{Lazardis:etal:2002}. A non
parameteric method is used to determine weights. The expression value
is then the weighted average. 

\section{Putting it altogether using {\tt expresso}}

The function that you should use is {\tt expresso}. It is important to
note that not every preprocessing method can be combined together. In
particular the \verb+rma+ backgrounds adjust only PM probe intensities
and so they should only be used in conjunction with the \verb+pmonly+
PM correction. Also remember that the \verb+mas+ and
\verb+medianpolish+ summarization methods $\log_2$ transform the data,
thus they should not be used in conjunction with any preprocessing
steps that are likely to yield negatives like the \verb+subtractmm+ pm
correction method. The following is a typical call to
\verb+expresso+. 

\begin{Sinput}
 library(affydata)
 data(Dilution)
 eset <- expresso(Dilution,bgcorrect.method="rma",
                  normalize.method="quantiles",
                  pmcorrect.method="pmonly",
                  summary.method="medianpolish")
\end{Sinput}
%@ 

This would give you the RMA expression measure, but of course there
are other ways of computing RMA (chiefly \verb+rma+). The true power
of \verb+expresso+ becomes apparent when you start combining different
methods. By choosing a method for each of the four steps ({\tt
  bgcorrect.method}, {\tt normalize.method}, {\tt pmcorrect.method},
{\tt summary.method}) you can create quite a variety of expression
measures. For instance 

\begin{Sinput}
eset <- expresso(Dilution,bgcorrect.method="mas",
                  normalize.method="qspline",
                  pmcorrect.method="subtractmm",
                  summary.method="playerout")
\end{Sinput}

would be a valid way of computing an expression measure (it is up to
the user to decide whether such a concoction is sensible or not). 


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