\Header{queryGEO}{Function to extract a data file from the GEO web site}
\keyword{manip}{queryGEO}
\begin{Description}\relax
Data files that are available at GEO web site are identified by GEO
accession numbers. Give a GEO object with the url for a common CGI and
a GEO accession number, this function extracts data from the web site
and returns a matrix containing the data portion of the file.\end{Description}
\begin{Usage}
\begin{verbatim}
queryGEO(GEOObj, GEOAccNum)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{GEOObj}] \code{GEOObj} a GEO object
\item[\code{GEOAccNum}] \code{GEOAccNum} a character string for the GEO
accession number of a desired file
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The GEO object contains the url for a CGI script that processes user's
request. \code{\Link{queryGEO}} invokes the CGI by passing a GEO
accession number and then processes the data file obtained.\end{Details}
\begin{Value}
\code{\Link{queryGEO}} returns a matrix containing data obtained.\end{Value}
\begin{Note}\relax
This function is part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{References}\relax
\url{www.ncbi.nlm.nih.gov/geo}\end{References}
\begin{SeeAlso}\relax
\code{\Link{GEO-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
geo <- GEO()
temp <- queryGEO(geo, "GPL49")
\end{ExampleCode}
\end{Examples}

