\HeaderA{dyebias.geo2marray}{convenience function to convert GEO objects to marray objects}{dyebias.geo2marray}
\keyword{misc}{dyebias.geo2marray}
\begin{Description}\relax
convenience function to convert GEO objects to marray objects
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{gse}] GSE data set 
\item[\code{slide.ids}] Return only the slides with these ids. If NULL,
return all.
\item[\code{type}] what to extract; must be either "norm" or "raw". 
\item[\code{gene.selector}] function(table) acting on Table(GPL) giving back 
an index with the rows considered to be genes. 
\item[\code{reporterid.name}] column containing the reporter.id, in Table(gpl).
\item[\code{cy3.name}] The column name containing the factor value for the Cy3
(green) channel 
\item[\code{cy5.name}] The column name containing the factor value for the Cy5
(red) channel 
\item[\code{R.name}] column name for extracting the R data from Table(gsm) 
\item[\code{G.name}] column name for extracting the G data from Table(gsm) 
\item[\code{M.name}] column name for extracting the M data from Table(gsm) 
\item[\code{A.name}] column name for extracting the A data from Table(gsm) 
\item[\code{Rf.name}] column name for extracting the Rf data from Table(gsm) 
\item[\code{Gf.name}] column name for extracting the Gf data from Table(gsm) 
\item[\code{Rb.name}] column name for extracting the Rb data from Table(gsm) 
\item[\code{Gb.name}] column name for extracting the Gb data from Table(gsm) 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \code{XYZ.name} mechanism is the same as that used in 
\code{\LinkA{read.marrayRaw}{read.marrayRaw}}; i.e. you specify the name of the
column that contains the desired data.
\end{Details}
\begin{Value}
A full-fledged  marrayRaw (if
\code{type} was "raw") or marrayNorm (if \code{type} was "norm") is returned.
\end{Value}
\begin{Note}\relax
At some point, this functionality should be merged into the
convert package.
\end{Note}
\begin{Author}\relax
Philip Lijnzaad
\end{Author}
\begin{References}\relax
Davis, S. and Meltzer, P.S (2007). GEOquery: a bridge
between the Gene Expression Omnibus (GEO) and BioConductor.
\emph{Bioinformatics} 23, 1846--1847 (doi:10.1093/bioinformatics/btm254).

Dudoit, S. and Yang, Y.H. (2002)  Bioconductor R packages for
exploratory analysis and normalization of cDNA microarray data. In:
Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger, S.L. (eds.)
\emph{The Analysis of Gene Expression Data: Methods and Software},
New\textasciitilde{}York: Springer

Chen,S., de\textasciitilde{}Vries, M.A. and Bell, S.P. (2007) \emph{Genes Dev.} 21, 2897--2907
"Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading"
(doi:10.1101/gad.1596807)
\end{References}
\begin{Examples}
\begin{ExampleCode}

                                       

## Not run: 
  ## Running this example takes too much time; if you want that, see the
  ## second example in the vignette
## End(Not run)                                       

\end{ExampleCode}
\end{Examples}

