\HeaderA{maigesRaw-class}{maigesRaw class, store raw microarray datasets}{maigesRaw.Rdash.class}
\aliasA{maigesRaw}{maigesRaw-class}{maigesRaw}
\keyword{classes}{maigesRaw-class}
\begin{Description}\relax
This class describes objects to handle intensity values and information
about genes and samples used in the data. Objects of this class are
obtained from class \code{\LinkA{maigesPreRaw}{maigesPreRaw}} using function
\code{\LinkA{createMaigesRaw}{createMaigesRaw}}.
\end{Description}
\begin{Details}\relax
This class of objects defines a real raw object that is used to do the
normalisation. Objects of this class are generated from objects of
class \code{\LinkA{maigesPreRaw}{maigesPreRaw}} using the function
\code{\LinkA{createMaigesRaw}{createMaigesRaw}}. Here it is possible to do several
plots for exploratory analysis using functions from
\emph{marray} package. Using the function
\code{\LinkA{selSpots}{selSpots}}, you select spots to use in the normalisation
method, that is done by the functions \code{\LinkA{normLoc}{normLoc}}, \code{\LinkA{normOLIN}{normOLIN}},
\code{\LinkA{normRepLoess}{normRepLoess}}, \code{\LinkA{normScaleLimma}{normScaleLimma}} and
\code{\LinkA{normScaleMarray}{normScaleMarray}}.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{Sf}:] numeric matrix containing the test samples
spots intensity values, spots corresponding to rows and data
tables (or chips) corresponding to columns.
\item[\code{Sb}:] numeric matrix containing the test samples
local background values, spots corresponding to rows and data
tables (or chips) corresponding to columns.
\item[\code{Sdye}:] character vector with length equal the length of
data files (chips), specifying the channel ('ch1' or 'ch2') used
to label each test sample in each chip.
\item[\code{Rf}:] numeric matrix containing the reference samples
spots intensity values, spots corresponding to rows and data
tables (or chips) corresponding to columns.
\item[\code{Rf}:] numeric matrix containing the reference samples
spots intensity values, spots corresponding to rows and data
tables (or chips) corresponding to columns.
\item[\code{Rdye}:] character vector with length equal the length of
data files (chips), specifying the channel ('ch1' or 'ch2') used
to label each reference sample in each chip.
\item[\code{Flag}:] matrix specifying the flags for the spots, as in
the matrices above, rows and columns correspond to genes and
samples, respectively. Type o value may be numeric or character,
depending of the flags used.
\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{UseSpots}:] logical matrix indexing the spots to be used
for normalisation.
\item[\code{GeneGrps}:] a logical matrix with rows representing the
spots and columns representing different gene groups. Each column
give the index of spots in that gene group.
\item[\code{Paths}:] list containing \code{\LinkA{graphNEL}{graphNEL}} objects
specifying gene regulatory networks (or pathways). The first
object in this list is a char string giving the gene label used to
match the genes.
\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{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[[] \code{signature(x = 'maigesRaw')}: subsetting operator for
spots on the array or arrays in the batch, ensures that all slots
are subset properly.
\item[boxplot] \code{signature(x = 'maigesRaw')}: boxplot method for
\code{\LinkA{maigesRaw}{maigesRaw}} class. Display boxplots of the slides and
print tip groups using package \emph{marray}.
\item[dim] \code{signature(x = 'maigesRaw', value = 'numeric')}: get
the dimensions of the object, numeric vector of length two.
\item[image] \code{signature(x = 'maigesRaw')}: image method for
\code{\LinkA{maigesRaw}{maigesRaw}} class. Display colour representation of
the slides using package \emph{marray}.
\item[plot] \code{signature(x = 'maigesRaw')}: plot method for
\code{\LinkA{maigesRaw}{maigesRaw}} class. Display \emph{MA} plots.
\item[print] \code{signature(x = 'maigesRaw')}: print method for
\code{\LinkA{maigesRaw}{maigesRaw}} class.
\item[show] \code{signature(x = 'maigesRaw')}: show method for
\code{\LinkA{maigesRaw}{maigesRaw}} class.
\item[summary] \code{signature(x = 'maigesRaw')}: summary method for
\code{\LinkA{maigesRaw}{maigesRaw}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{createMaigesRaw}{createMaigesRaw}}, \code{\LinkA{selSpots}{selSpots}},
\code{\LinkA{normLoc}{normLoc}}, \code{\LinkA{normOLIN}{normOLIN}},
\code{\LinkA{normRepLoess}{normRepLoess}}, \code{\LinkA{normScaleLimma}{normScaleLimma}} and
\code{\LinkA{normScaleMarray}{normScaleMarray}}.
\end{SeeAlso}

