\HeaderA{readHeader}{Read Header Information from Image Analysis Raw Data File}{readHeader}
\aliasA{readGenericHeader}{readHeader}{readGenericHeader}
\aliasA{readGPRHeader}{readHeader}{readGPRHeader}
\aliasA{readSMDHeader}{readHeader}{readSMDHeader}
\keyword{file}{readHeader}
\begin{Description}\relax
Read the header information from a GenePix Results (GPR) file or from an SMD raw data file.
These functions are used internally by \code{read.maimages} and are not usually called directly by users.
\end{Description}
\begin{Usage}
\begin{verbatim}
readGenericHeader(file, columns, sep="\t")
readGPRHeader(file)
readSMDHeader(file)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{file}] character string giving file name. If it does not contain an absolute path, the file name is relative to the current working directory.
\item[\code{columns}] character vector specifying data column headings expected to be in file
\item[\code{sep}] the character string separating column names
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Raw data files exported by image analysis programs include a number of header lines which contain information about the scanning process.
This function extracts that information and locates the line where the intensity data begins.
\code{readGPRHeader} is for GenePix output and \code{readSMDHeader} is for files from the Stanford Microarray Database (SMD).
\code{readGenericHeader} finds the line in the file on which the data begins by searching for specified column headings.
\end{Details}
\begin{Value}
A list with components corresponds to lines of header information.
A key component is \code{NHeaderRecords} which gives the number of lines in the file before the intensity data begins.
All other components are character vectors.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{References}\relax
See \url{http://www.axon.com/gn_GenePix_File_Formats.html} for GenePix formats.

See \url{http://www.bluegnome.co.uk} for information on BlueFuse.

See \url{http://genome-www.stanford.edu/Microarray} for the SMD.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{read.maimages}{read.maimages}}

An overview of LIMMA functions to read data is given in \LinkA{03.ReadingData}{03.ReadingData}.
\end{SeeAlso}

