\name{read.affy.mixed}
\alias{read.affy.mixed}

\title{ Read a Set of .CEL Files and Phenotypic Data from mixed chip types}
\description{
 Reads the specified file, which defines phenotypic data for a
 set of .CEL files. Reads the specified files into an \code{\link[affy]{AffyBatch}} object and
 then creates a \code{\link[Biobase]{phenoData}} object, defining the experimental factors 
 for those chips. This function deals with different array types by generating a pseudo arrayset containing only the probes in common. It does this by finding the smallest chip type in the set, and using this as a template. Probesets that aren't shared are set to 0. Other probesets are copied in. Note that this means that spots that were in one place on one array, appear to be at a different place on another. What this does to position specific background correction algorithms (such as mas5) is left as an exercise to the reader). Beware...
}
\usage{
read.affy.mixed(covdesc = "covdesc",path=".", ...)
}

\arguments{
  \item{covdesc}{ 
    A white space delimited file suitable for reading as a \code{\link{data.frame}}. The first column (with no column name)  
     contains the names(or paths to) the .CEL files to read. Remaining columns (with names) represent experimental factors
     for each chip. these become elements of the \code{\link[Biobase]{phenoData}} object.
  }
  \item{\dots}{ extra functions to pass on to \code{ReadAffy} }
  \item{path}{ The path to prefix the filenames with before calling \code{ReadAffy} }
}
\details{ }
\value{
  An AffyBatch object
}
\references{\url{ http://bioinformatics.picr.man.ac.uk/}}
\author{ Crispin J Miller }

\seealso{ \code{\link[affy]{ReadAffy}}, \code{\link[affy]{AffyBatch}} \code{\link{data.frame}} \code{\link[Biobase]{phenoData}}}
\keyword{ misc }
\examples{ 
  \dontrun{
    eset <- read.affy.mixed(); # read a set of CEL files
  
    eset.rma <- call.exprs(eset,"rma");   
  }
}