\name{affystart}
\alias{affystart}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Pre-processing for Affymetrix Data}
\description{
  This function is designed to automatically read in all cel files in a
  directory, make all pre-processing QC plots and compute expression measures.
}
\usage{
affystart(\dots, filenames=NULL, groups = NULL, groupnames = NULL, plot =
TRUE, pca = TRUE,  squarepca = FALSE, plottype="pdf", express = c("rma",
"mas5", "gcrma"), addname = NULL, output = "txt", annotate =
FALSE, ann.vec =  c("SYMBOL","GENENAME","ENTREZID","UNIGENE","REFSEQ"))
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{\dots}{Requires that all variables be named.}
  \item{filenames}{If not all cel files in a directory will be used,
    pass a vector of filenames.}
  \item{groups}{An integer \code{vector} indicating the group assignments
    for the PCA plot.}
  \item{groupnames}{A character \code{vector} with group names for PCA
    legend.}
  \item{plottype}{What type of plot to save. Can be "pdf","postscript",
    "png","jpeg", or "bmp". Defaults to "pdf". Note that "png" and
    "jpeg" may not be available on a given computer. See the help page
    for \code{capabilities} and  \code{png} for more information.}
  \item{plot}{Should density and degradation plots be made? Defaults to
    \code{TRUE}.}
  \item{pca}{Should a PCA plot be made? Defaults to \code{TRUE}. }
  \item{squarepca}{Should the y-axis of the PCA plot be made comparable
    to the x-axis? This may aid in interpretation of the PCA plot. 
    Defaults to \code{FALSE}.}
  \item{express}{One of either rma, mas5, gcrma. Defaults to rma.
    Partial matching OK.}
  \item{addname}{Used to append something to the name of the pca plot
    and the expression values output file (e.g., if function is run
    twice using different methods to compute expression values).}
  \item{output}{What format to use for the output of expression
    values. Currently only supports text format.}
  \item{annotate}{Boolean. Add annotation data to the output file?}
  \item{ann.vec}{A character \code{vector} of annotation data to add to the
    output file.}
 }

\value{
  Returns an \code{ExpressionSet}.
}
\seealso{\code{plotHist}, \code{plotDeg}, \code{plotPCA}
}
\author{James W. MacDonald <jmacdon@med.umich.edu>}
\keyword{hplot}% at least one, from doc/KEYWORDS
\keyword{manip}% __ONLY ONE__ keyword per line