\HeaderA{addNormToMAGEML}{Adding a norm object to an existing MAGEML document}{addNormToMAGEML}
\keyword{methods}{addNormToMAGEML}
\begin{Description}\relax
This function adds normalised data object obtained with limma or marray package to a MAGEML document.
\end{Description}
\begin{Usage}
\begin{verbatim}
addNormToMAGEML(mageOM = NULL, norm = NULL, outputDirectory = ".",
externalDataFiles = NULL, protocolID = NULL, protocol = "none", date="NA", qtID =
NULL, qtName = NULL, qtScale = NULL, qtDataType = NULL, qtDimID =
NULL,transformationID = NULL, DED = "none", BADIDs = NULL, derivedBioAssayIDs = NULL, derivedBioAssayDataIDs = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{norm}] Normalised limma (MAList) or marray (marrayNorm) object
\item[\code{mageOM}] Reference to MAGE Object Model, generated by
importMAGEOM() method.
\item[\code{outputDirectory}] Directory where updated MAGEML document will
be written to
\item[\code{externalDataFiles}] List of names for external data files
associated with a DerivedBioAssayData object.  Each filename should
end with .txt as this is the standard output file format
\item[\code{protocolID}] ID you want to give to the protocol, e.g. P-normalised-1
\item[\code{protocol}] Describiption of the used protocol
\item[\code{date}] Date when protocol was applied
\item[\code{qtID}] Identifier used for the QuantitationType (the normalised
value)
\item[\code{qtName}] Name for the QuantitationType
\item[\code{qtScale}] Scale of the QuantitationType, e.g. linear
\item[\code{qtDataType}] DataType of the QuantitationType e.g. scalar
\item[\code{qtDimID}] A new QuantitationTypeDimension will be generated
you'll have to specify it's identifier
\item[\code{transformationID}] Identifier for the applied transformation e.g.
TFM:1
\item[\code{DED}] DesignElementDimension corresponding to the features that
are present in the normalised object, if only one dimension present
in original MAGEML file then this parameter should not be specified
\item[\code{BADIDs}] List of BioAssayData identifier
\item[\code{derivedBioAssayIDs}] List of identifiers for the DerivedBioAssay e.g. DBA-1
\item[\code{derivedBioAssayDataIDs}] List of identifiers for the DerivedBioAssayData
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Steffen Durinck, \url{http://www.esat.kuleuven.ac.be/~sdurinck}\\ 
Joke Allemeersch, \url{http://www.esat.kuleuven.ac.be/~jallemee}.
\end{Author}
\begin{References}\relax
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr and Brazma A.
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome Biol. 2002 Aug 23;3(9):RESEARCH0046.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{importMAGEOM}{importMAGEOM}},\code{\LinkA{writeMAGEML}{writeMAGEML}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
#library(RMAGEML)
#raw<- importMAGEML(directory = "/home/steffen/data/MEXP-14")
#norm<-maNorm(raw)
#mageom <- importMAGEOM(directory = "/home/steffen/data/MEXP-14")
#outputDirectory <- "/home/steffen/XMLout"
#externalDataFile <- "deriv_test.txt"
#protocolID <- "P-CAGE-test"
#protocol <- "This is a test protocol! Applied maNorm."
#qtID <- c("esat.kuleuven.ac.be:quantT-1-test", "esat.kuleuven.ac.be:quantT-2-test")
#qtName <- c("quantitation Name 1", "quantitation Name 2")
#qtScale <- c("linear","linear")
#qtDataType <- c("scalar","scalar")
#qtDimID <- "esat.kuleuven.ac.be:QTD-test"
#BADIDs <- c("esat.kuleuven.ac.be:BAD-test1","esat.kuleuven.ac.be:BAD-test2")
#derivedBioAssayIDs <- c("esat.kuleuven.ac.be:DBA-test1","esat.kuleuven.ac.be:DBA-test2")
#derivedBioAssayDataIDs <- c("esat.kuleuven.ac.be:DBD-test1", "esat.kuleuven.ac.be:DBD-test2")
#addNormToMAGEML(mageOM = mageom, norm = norm, outputDirectory = outputDirectory, externalDataFile = externalDataFile, protocolID = protocolID, protocol = protocol,  qtID = qtID, qtName = qtName, qtScale = qtScale, qtDataType = qtDataType, qtDimID = qtDimID, DED = "none", BADIDs = BADIDs, derivedBioAssayIDs = derivedBioAssayIDs, derivedBioAssayDataIDs = derivedBioAssayDataIDs)

\end{ExampleCode}
\end{Examples}

