\HeaderA{read.exprSet}{Read Experimental Data and into an 'exprSet' Object}{read.exprSet}
\keyword{file}{read.exprSet}
\keyword{manip}{read.exprSet}
\begin{Description}\relax
An exprSet object has a slot named \code{exprs} for experimental data. \code{read.exprSet} reads the experimental data stored as a text file and then generates an exprSet object using the data. Data for other slots can be also read in as options.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.exprSet(exprs, se.exprs, phenoData, annotation, description, notes, seps = "\t")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{exprs}] \code{exprs} a character string for the name of the text file that stores the experimental data to be read in. The text file is assumed to be a delimited file with observed expression levels arranged in rows and columns. The first row of the file is sample names and the first column is gene names/ids. The file will be read in using read.table with header set to TRUE
\item[\code{se.exprs}] \code{se.exprs} a character stirng for the name of a delimited text file contains standard error estimates for the estimated expression in exprs. The file is of the same dimensions as 'exprs'
\item[\code{phenoData}] \code{phenoData} a character string for the name of an optional file containing information for 'pData' slot of a phenoData object to be returned. If missing a default phenoData object with one covariate ranging from 1 to the number of columns of 'exprs' will be provided
\item[\code{annotation}] \code{annotation} a character string for the name of an optional text file that contains a string identifying the annotation that may be used for the 'exprSet' instance
\item[\code{description}] \code{description} a character string for the name of an optional file containing MIAME information
\item[\code{notes}] \code{notes} a character string for the name of an optional text file containing explanatory text
\item[\code{seps}] \code{seps} a vector of character strings defining the delimitors used by 'exprs' and 'se.exprs'. The length of 'seps' can be 1 when both file have the same delimiter or 'se.exprs' is missing or 2 other wise. The delimitor for 'exprs' is expected to be the first element
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If not missing, 'phenoData' will be read in using \code{\LinkA{read.phenoData}{read.phenoData}} and description using
\code{\LinkA{read.MIAME}{read.MIAME}}. The help files of the two functions contain detailed descriptions of the two functions.
\end{Details}
\begin{Value}
This function returns an \code{exprSet} object.
\end{Value}
\begin{Author}\relax
Jianhua Zhang
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{exprSet}{exprSet}}, \code{\LinkA{phenoData}{phenoData}}, \code{\LinkA{MIAME}{MIAME}}, \code{\LinkA{read.phenoData}{read.phenoData}}, \code{\LinkA{read.MIAME}{read.MIAME}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Creating a test data
testFile <- tempfile()
data(geneData)
write.table(geneData, testFile, quote = FALSE, sep = "\t", row.names =
TRUE, col.names = TRUE)
# Create an exprSet object using textFile
eSet <- read.exprSet(testFile)
eSet
\end{ExampleCode}
\end{Examples}

