\HeaderA{maigesPreRaw-class}{maigesPreRaw class, store pre raw microarray datasets}{maigesPreRaw.Rdash.class}
\aliasA{maigesPreRaw}{maigesPreRaw-class}{maigesPreRaw}
\keyword{classes}{maigesPreRaw-class}
\begin{Description}\relax
This class describes objects to handle data values and information
about genes and samples used in the data. Here, it is possible to put
any field from data tables that you want.
\end{Description}
\begin{Details}\relax
This class of objects is intended to define an intermediate step
between the external world (data tables, gene groups, gene networks,
etc) and real raw objects given by the class
\code{\LinkA{maigesRaw}{maigesRaw}}. In this intermediate step the user can do any
type of exploratory analysis and set bad spots (at slot
\code{BadSpots}), or to do any type of calculation they judge
important in the fields of \code{Data} slot.

This class of objects is created by a call from
\code{\LinkA{loadData}{loadData}}. The functions \code{\LinkA{addGeneGrps}{addGeneGrps}} and
\code{\LinkA{addPaths}{addPaths}} may also be used to add information for gene
groups and gene networks. After the exploratory analysis it must be
converted in an object of class \code{\LinkA{maigesRaw}{maigesRaw}} using the
function \code{\LinkA{createMaigesRaw}{createMaigesRaw}}.

If you have the package \emph{Rgraphviz} installed and working it is
possible to display the graphs stored in the slot \code{Paths} using
the command \code{\LinkA{plot}{plot}}.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{Data}:] contains a list with matrices. Each matrix has
\code{nrow} = number of spots and \code{ncol} = number of data
tables (or chips) with the numerical values of each data field
specified by the user in the configuration file used as parameter
for \code{\LinkA{loadData}{loadData}} function.
\item[\code{GeneGrps}:] a list containing character vectors. These
vectors specify genes from the gene groups that must be
studied. Each vector is used as a gene group. The names of the
groups are catch from the names of the vectors from the list,
that is catch from file names.
\item[\code{Paths}:] list containing \code{\LinkA{graphNEL}{graphNEL}} objects
specifying gene regulatory networks (or pathways). As in the
previous slot, the names are catch from file names and stored as
names of the elements from the list.
\item[\code{Layout}:] a list containing the number of rows (\code{gridR}) and
columns (\code{gridC}) of grids, the number of rows (\code{spotR})
and columns (\code{spotC}) of spots inside each grid and the total
number of spots.
\item[\code{Glabels}:] data frame giving the gene labels. These
labels are generally used during the data analysis.
\item[\code{Slabels}:] data frame giving the sample labels. These
labels are generally used during the data analysis.
\item[\code{BadSpots}:] logical vector specifying spots that was
judged as bad ones. By default this slot is created as a vector of
FALSEs with same length as number of spots.
\item[\code{Notes}:] char string that receives any comment about the
dataset. The dataset description is stored in this slot.
\item[\code{Date}:] char string giving the date and hour that the
object was created.
\item[\code{V.info}:] list containg three characters. The first one is
a string containing the R version used when the object was
created. The second is a char vector with base packages and the
last one is another char vector with additional packages and
version numbers.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[print] \code{signature(x = 'maigesPreRaw')}: print method for
\code{\LinkA{maigesPreRaw}{maigesPreRaw}} class.
\item[show] \code{signature(x = 'maigesPreRaw')}: show method for
\code{\LinkA{maigesPreRaw}{maigesPreRaw}} class.
\item[summary] \code{signature(x = 'maigesPreRaw')}: summary method for
\code{\LinkA{maigesPreRaw}{maigesPreRaw}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{loadData}{loadData}}, \code{\LinkA{addGeneGrps}{addGeneGrps}},
\code{\LinkA{addPaths}{addPaths}}, \code{\LinkA{createMaigesRaw}{createMaigesRaw}}.
\end{SeeAlso}

