\Header{PLMset-class}{Class PLMset}
\alias{boxplot,PLMset-method}{PLMset-class}
\alias{cdfName,PLMset-method}{PLMset-class}
\alias{coefs}{PLMset-class}
\alias{coefs,PLMset-method}{PLMset-class}
\alias{coefs.const}{PLMset-class}
\alias{coefs.const,PLMset-method}{PLMset-class}
\alias{coefs.probe}{PLMset-class}
\alias{coefs.probe,PLMset-method}{PLMset-class}
\alias{coefs<\Rdash}{PLMset-class}
\alias{coefs<-,PLMset-method}{PLMset-class}
\alias{getCdfInfo,PLMset-method}{PLMset-class}
\alias{image,PLMset-method}{PLMset-class}
\alias{indexProbes,PLMset,character-method}{PLMset-class}
\alias{indexProbesProcessed}{PLMset-class}
\alias{indexProbesProcessed,PLMset-method}{PLMset-class}
\alias{Mbox}{PLMset-class}
\alias{Mbox,PLMset-method}{PLMset-class}
\alias{model.description}{PLMset-class}
\alias{model.description,PLMset-method}{PLMset-class}
\alias{normvec}{PLMset-class}
\alias{normvec,PLMset-method}{PLMset-class}
\alias{PLMset}{PLMset-class}
\alias{resid,PLMset-method}{PLMset-class}
\alias{resid<\Rdash}{PLMset-class}
\alias{resid<-,PLMset-method}{PLMset-class}
\alias{residSE}{PLMset-class}
\alias{residSE,PLMset-method}{PLMset-class}
\alias{residuals,PLMset-method}{PLMset-class}
\alias{residuals<\Rdash}{PLMset-class}
\alias{residuals<-,PLMset-method}{PLMset-class}
\alias{sampleNames<\Rdash}{PLMset-class}
\alias{sampleNames<-,PLMset-method}{PLMset-class}
\alias{se}{PLMset-class}
\alias{se,PLMset-method}{PLMset-class}
\alias{se.const}{PLMset-class}
\alias{se.const,PLMset-method}{PLMset-class}
\alias{se.probe}{PLMset-class}
\alias{se.probe,PLMset-method}{PLMset-class}
\alias{se<\Rdash}{PLMset-class}
\alias{se<-,PLMset-method}{PLMset-class}
\alias{show,PLMset-method}{PLMset-class}
\alias{summary,PLMset-method}{PLMset-class}
\alias{varcov}{PLMset-class}
\alias{varcov,PLMset-method}{PLMset-class}
\alias{weights,PLMset-method}{PLMset-class}
\alias{weights<\Rdash}{PLMset-class}
\alias{weights<-,PLMset-method}{PLMset-class}
\keyword{classes}{PLMset-class}
\begin{Description}\relax
This is a class representation for Probe level Linear
Models fitted to Affymetrix GeneChip probe level data.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created using the function \code{\Link{fitPLM}}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{probe.coefs}:] Object of class "matrix". Contains model
coefficients related to probe effects
\item[\code{se.probe.coefs}:] Object of class "matrix". Contains
standard error estimates for the probe coefficients  
\item[\code{chip.coefs}:] Object of class "matrix". Contains model
coefficients related to chip (or chip level) effects for each fit.
\item[\code{se.chip.coefs}:] Object of class "matrix". Contains
standard error estimates for the chip coefficients
\item[\code{model.description}:] Object of class "character". This
string describes the probe level model fitted.
\item[\code{weights}:] Object of class "matrix". Contains probe
weights for each fit. The matrix has columns for chips and rows
are probes
\item[\code{phenoData}:] Object of class "phenoData" This is an
instance of class \code{phenoData} 
containing the patient (or case) level data. The columns of the
pData slot of this entity represent
variables and the rows represent patients or cases. 
\item[\code{annotation}] A character string identifying the
annotation that may be used for the \code{exprSet} instance.
\item[\code{description}:] Object of class "MIAME". For
compatibility with previous version of this class description can
also be a "character". The class \code{characterOrMIAME} has been
defined just for this.
\item[\code{cdfName}:] A character string giving the name of the
cdfFile
\item[\code{nrow}:] Object of class "numeric". Number of rows in chip
\item[\code{ncol}:] Object of class "numeric". Number of cols in chip
\item[\code{notes}:] Object of class "character" Vector of
explanatory text 
\item[\code{varcov}:] Object of class "list". A list of
variance/covariance matrices
\item[\code{residualSE}:] Object of class "matrix". Contains residual
standard error and df
\item[\code{residuals}:] Object of class "matrix". Contains
residuals from model fit (if stored)
}
\end{Section}
\begin{Section}{Extends}
Class \code{"exprSet"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[weights<-] \code{signature(object = "PLMset")}: replaces the weights 
\item[weights] \code{signature(object = "PLMset")}: extracts the
model fit weights
\item[coefs<-] \code{signature(object = "PLMset")}: replaces the
chip coefs.  
\item[coefs] \code{signature(object = "PLMset")}: extracts the
chip coefs. 
\item[se] \code{signature(object = "PLMset")}: extracts the
standard error estimates of the chip coefs. 
\item[se<-] \code{signature(object = "PLMset")}: replaces the
standard error estimates of the chip coefs. 
\item[coefs.probe] \code{signature(object = "PLMset")}: extracts the
probe coefs. 
\item[se.probe] \code{signature(object = "PLMset")}: extracts the standard error estimates of the probe coefs.     
\item[coefs.const] \code{signature(object = "PLMset")}: extracts the
intercept coefs. 
\item[se.const] \code{signature(object = "PLMset")}: extracts the standard error estimates of the intercept coefs. 
\item[getCdfInfo] \code{signature(object = "PLMset")}: retrieve
the environment that defines the location of probes by probe set. 
\item[image] \code{signature(x = "PLMset")}: creates an
image of the robust linear model fit weights for
each sample.
\item[indexProbes] \code{signature(object = "PLMset", which =
        "character")}: returns a list with locations of the probes in
each probe  set. The list names defines the probe set
names. \code{which} can be "pm", "mm", or "both". If "both" then
perfect match locations are given followed by mismatch locations.
\item[Mbox] \code{signature(object = "PLMset")}: gives a boxplot of
M's for each chip. The M's are computed relative to a "median"
chip.
\item[normvec] will return the normalization vector (if it has been
stored)
\item[residSE] will return the residual SE (if it has been stored)
}
\end{Section}
\begin{Note}\relax
This class is better described in the vignette.
\end{Note}
\begin{Author}\relax
B. M. Bolstad \email{bolstad@stat.berkeley.edu}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

