\HeaderA{produceGEOSubmissionFile}{Produce GEO Sample Submission File in SOFT format}{produceGEOSubmissionFile}
\keyword{utilities}{produceGEOSubmissionFile}
\begin{Description}\relax
Produce GEO Sample Submission File in the SOFT format based on the provided LumiBatch object and sample information
\end{Description}
\begin{Usage}
\begin{verbatim}
produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib.mapping = NULL, idType = 'Probe', sampleInfo = NULL, fileName = "GEOSubmissionFile.txt", supplementaryRdata = TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{lumiNormalized}] The normalized data (LumiBatch object) 
\item[\code{lumiRaw}] The raw data (LumiBatch object), e.g., returned by \code{\LinkA{lumiR}{lumiR}} 
\item[\code{lib.mapping}] The Illumina ID Mapping library, e.g., "lumiHumanIDMapping" 
\item[\code{idType}] the idType parameter of function \code{\LinkA{nuID2IlluminaID}{nuID2IlluminaID}} 
\item[\code{sampleInfo}] The sample information filename or data.frame, which is returned by \code{\LinkA{produceGEOSampleInfoTemplate}{produceGEOSampleInfoTemplate}} 
\item[\code{fileName}] The file name of GEO Submission file  
\item[\code{supplementaryRdata}] determine whether produce the Rdata supplement data, which include both lumiNormalized and lumiRaw R objects. 
\item[\code{...}] other parameters used by function \code{\LinkA{nuID2IlluminaID}{nuID2IlluminaID}} 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function produces the GEO sample submission file including both normalized and raw data information  in the SOFT format. The sample information should be provided by the user as a data.frame or Tab separated text file following the format of the template, which can be produced by function \code{\LinkA{produceGEOSampleInfoTemplate}{produceGEOSampleInfoTemplate}}. Users need to fill in the detailed sample descriptions in the template, especially the Sample\_title, Sample\_description and some protocols. Users are also suggested to fill in the "Sample\_platform\_id" by checking information of the GEO Illumina platform.

When the parameter "supplementaryRdata" is TRUE, the R objects, lumiNormalized, lumiRaw and sampleInfo, will be saved in a file named 'supplementaryData.Rdata'.
\end{Details}
\begin{Value}
Save the result as a text file in SOFT sample submission format. The supplementary Rdata will be saved in a file 'supplementaryData.Rdata'.
\end{Value}
\begin{Author}\relax
Pan Du
\end{Author}
\begin{References}\relax
http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{produceGEOSampleInfoTemplate}{produceGEOSampleInfoTemplate}}, \code{\LinkA{produceGEOPlatformFile}{produceGEOPlatformFile}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run
## Produce the sample information template
# produceGEOSampleInfoTemplate(lumiNormalized, lib.mapping = NULL, fileName = "GEOsampleInfo.txt")
## After editing the 'GEOsampleInfo.txt' by filling in sample information
# produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib='lumiHumanIDMapping', sampleInfo='GEOsampleInfo.txt')
\end{ExampleCode}
\end{Examples}

