\HeaderA{Converting}{Convert a GDS datastructure to a BioConductor datastructure}{Converting}
\aliasA{GDS2eSet}{Converting}{GDS2eSet}
\aliasA{GDS2MA}{Converting}{GDS2MA}
\keyword{IO}{Converting}
\begin{Description}\relax
Functions to take a GDS data structure from getGEO and coerce it to
limma MALists or exprSets.
\end{Description}
\begin{Usage}
\begin{verbatim}
GDS2MA(GDS,do.log2=FALSE,GPL=NULL)
GDS2eSet(GDS,do.log2=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{GDS}] The GDS datastructure returned by getGEO
\item[\code{do.log2}] Boolean, should the data in the GDS be log2 transformed
before inserting into the new data structure
\item[\code{GPL}] Either a GPL data structure (from a call to getGEO) or
NULL.  If NULL, this will cause a call to getGEO to produce a GPL.
The gene information from the GPL is then used to construct the
\code{genes} slot of the resulting limma \code{MAList} object.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function just rearranges one data structure into another.  For
GDS, it also deals appropriately with making the "targets" list item
for the limma data structure and the phenoData slot of exprSets.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{GDS2MA}] A limma MAList
\item[\code{GDS2eSet}] A exprSet object
\end{ldescription}
\end{Value}
\begin{Author}\relax
Sean Davis
\end{Author}
\begin{References}\relax
See the limma and exprSet help in the appropriate packages
\end{References}
\begin{Examples}
\begin{ExampleCode}

## Not run: gds505 <- getGEO('GDS505')
## Not run: MA <- GDS2MA(gds505)
## Not run: eset <- GDS2eSet(gds505)

\end{ExampleCode}
\end{Examples}