\HeaderA{maiges-class}{maiges class, store normalised microarray datasets}{maiges.Rdash.class}
\aliasA{maiges}{maiges-class}{maiges}
\keyword{classes}{maiges-class}
\begin{Description}\relax
This class describes objects to handle ratio of intensities (\emph{W})
and average of intensities (\emph{A}) values values and information
about genes and samples used in the data. Objects of this class are
created from class \code{\LinkA{maigesRaw}{maigesRaw}} using the functions
\code{\LinkA{normLoc}{normLoc}}, \code{\LinkA{normOLIN}{normOLIN}},
\code{\LinkA{normRepLoess}{normRepLoess}}, \code{\LinkA{normScaleLimma}{normScaleLimma}} and/or
\code{\LinkA{normScaleMarray}{normScaleMarray}} to do the normalisation.

Here, the \emph{M=log(R/G)} value of intensity ratio was redefined as
\emph{W=log(Test/Ref)}, where \emph{Test} and \emph{Ref} are the test
and reference samples.
\end{Description}
\begin{Details}\relax
This defines the main class of objects defined in
this package. It is created from \code{\LinkA{maigesRaw}{maigesRaw}} class
using the normalisation functions \code{\LinkA{normLoc}{normLoc}}, \code{\LinkA{normOLIN}{normOLIN}},
\code{\LinkA{normRepLoess}{normRepLoess}}, \code{\LinkA{normScaleLimma}{normScaleLimma}} and
\code{\LinkA{normScaleMarray}{normScaleMarray}}. From this class
of objects it is possible to do any type of analysis defined by
several functions in this package. Also, it is possible to summarise
spots (or samples) information using the function
\code{\LinkA{summarizeReplicates}{summarizeReplicates}}.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{W}:] numeric matrix containing the ratio values (in log2
scale) between the test and reference sample intensities (W
values). Spots are indexed by rows and samples by columns.
\item[\code{A}:] numeric matrix containing the mean intensity
values between test and reference samples (also in log2 scale). 
Spots corresponding to rows and samples (or chips) corresponding
to columns, too.
\item[\code{SD}:] numeric matrix containing the standard deviation
of W values when the lowess step is repeated several times.
\item[\code{IC1}:] numeric matrix containing the left margin of
confidence interval defined by repeated lowess during the
normalisation step.
\item[\code{IC2}:] numeric matrix containing the right margin of
confidence interval defined above.
\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 = 'maiges')}: subsetting operator for
spots on the array or arrays in the batch, ensures that all slots
are subset properly.
\item[boxplot] \code{signature(x = 'maiges')}: boxplot method for
\code{\LinkA{maiges}{maiges}} class. Display boxplots of the slides and
print tip groups using package \emph{marray} or boxplots of
one gene previously defined.
\item[dim] \code{signature(x = 'maiges', value = 'numeric')}: get
the dimensions of the object, numeric vector of length two.
\item[image] \code{signature(x = 'maiges')}: image method for
\code{\LinkA{maiges}{maiges}} class. Display colour representation of
the slides using package \emph{marray}.
\item[plot] \code{signature(x = 'maiges')}: plot method for
\code{\LinkA{maiges}{maiges}} class. Display 'MA' plots.
\item[print] \code{signature(x = 'maiges')}: print method for
\code{\LinkA{maiges}{maiges}} class.
\item[show] \code{signature(x = 'maiges')}: show method for
\code{\LinkA{maiges}{maiges}} class.
\item[summary] \code{signature(x = 'maiges')}: summary method for
\code{\LinkA{maiges}{maiges}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{normLoc}{normLoc}}, \code{\LinkA{normOLIN}{normOLIN}},
\code{\LinkA{normRepLoess}{normRepLoess}}, \code{\LinkA{normScaleLimma}{normScaleLimma}},
\code{\LinkA{normScaleMarray}{normScaleMarray}} and \code{\LinkA{summarizeReplicates}{summarizeReplicates}}.
\end{SeeAlso}

