\HeaderA{validTreetype}{Validate Tree Type}{validTreetype}
\keyword{manip}{validTreetype}
\begin{Description}\relax
Validate tree type for corresponding data type.
\end{Description}
\begin{Usage}
\begin{verbatim}
validTreetype(treetype, datatype)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{treetype}] tree type.
\item[\code{datatype}] data type.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Every \code{\LinkA{ROOT}{ROOT}} tree has an extension, which describes the type of data stored in this tree.
For example, \sQuote{TestA1.cel} is the tree name that stores the CEL-file data for \sQuote{TestA1.CEL}.

Trees with \code{datatype="scheme"} have the following extensions: \\
\code{scm}: scheme tree containing (x,y)-coordinates and mask for UNIT\_ID. \\
\code{idx}: unit tree containing UnitName (i.e. probeset id), NumCells, NumAtoms, UnitType, for UNIT\_ID. \\
\code{prb}: probe tree containing probe sequences. \\
\code{ann}: transcript annotation tree. \\
\code{anx}: exon annotation tree; exon arrays only. \\
\code{anp}: probeset annotation tree; exon arrays only. \\
\code{cxy}: coordinate tree containing CLF-file information; exon arrays only. \\
\code{exn}: exon tree; exon arrays only. \\
\code{pbs}: probeset tree; exon arrays only. 

Trees with \code{datatype="rawdata"} have the following extensions: \\
\code{cel}: data tree containing CEL-file data.

Trees with \code{datatype="preprocess"} have the following extensions: \\
\code{int}: intensity tree containing background-corrected intensities. \\
\code{sbg}: background tree containing MAS4 sector background levels. \\
\code{wbg}: background tree containing MAS5 weighted sector background levels. \\
\code{rbg}: background tree containing RMA background levels. \\
\code{gbg}: background tree containing GC-content background levels. \\
\code{cmn}: cell tree containing preprocessed intensities using algorithm \sQuote{mean}. \\
\code{cmd}: cell tree containing preprocessed intensities using algorithm \sQuote{median}. \\
\code{clw}: cell tree containing preprocessed intensities using algorithm \sQuote{lowess}. \\
\code{css}: cell tree containing preprocessed intensities using algorithm \sQuote{supsmu}. \\
\code{cqu}: cell tree containing preprocessed intensities using algorithm \sQuote{quantile}. \\
\code{dc5}: detection tree containing MAS5 detection call and p-value. \\
\code{dab}: detection tree containing DABG detection call and p-value. \\
\code{amn}: expression tree containing expression levels computed with \sQuote{arithmetic mean}. \\
\code{gmn}: expression tree containing expression levels computed with \sQuote{geometric mean}. \\
\code{wmn}: expression tree containing expression levels computed with \sQuote{weighted mean}. \\
\code{wdf}: expression tree containing expression levels computed with \sQuote{weighted difference}. \\
\code{adf}: expression tree containing expression levels computed with \sQuote{average difference}. \\
\code{tbw}: expression tree containing expression levels computed with \sQuote{tukey biweight}. \\
\code{mdp}: expression tree containing expression levels computed with \sQuote{median polish}. \\

Trees with \code{datatype="normation"} have the following extensions: \\
\code{tmn}: expression tree after normalization using algorithm \sQuote{trimmed mean}. \\
\code{med}: expression tree after normalization using algorithm \sQuote{median}. \\
\code{ksm}: expression tree after normalization using algorithm \sQuote{kernel smoother}. \\
\code{low}: expression tree after normalization using algorithm \sQuote{lowess}. \\
\code{sup}: expression tree after normalization using algorithm \sQuote{supsmu}. \\
\code{qua}: expression tree after normalization using algorithm \sQuote{quantile}. \\
\code{mdp}: expression tree after normalization using algorithm \sQuote{median polish}.
\end{Details}
\begin{Value}
Returns the valid \code{treetype}, otherwise an error message is returned.
\end{Value}
\begin{Note}\relax
Not all tree types are used in the current package.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getDatatype}{getDatatype}}, \code{\LinkA{type2Exten}{type2Exten}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
validTreetype("prb", "scheme")
validTreetype("cel", "rawdata")
validTreetype("tbw", "preprocess")
\end{ExampleCode}
\end{Examples}

