\HeaderA{avedups}{Average Over Duplicate Spots}{avedups}
\methaliasA{avedups.default}{avedups}{avedups.default}
\methaliasA{avedups.MAList}{avedups}{avedups.MAList}
\keyword{array}{avedups}
\begin{Description}\relax
Condense a microarray data object so that values for within-array replicate spots are replaced with their average.
\end{Description}
\begin{Usage}
\begin{verbatim}
## Default S3 method:
avedups(x, ndups=2, spacing=1, weights=NULL)
## S3 method for class 'MAList':
avedups(x, ndups=x$printer$ndups, spacing=x$printer$spacing, weights=x$weights)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a matrix-like object, usually a matrix or an \code{MAList} object.
\item[\code{ndups}] number of within-array replicates for each probe.
\item[\code{spacing}] number of spots to step from a probe to its duplicate.
\item[\code{weights}] numeric matrix of spot weights.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
A new data object is computed in which each probe is represented by the (weighted) average of its duplicate spots.
For a \code{MAList} object, the components \code{M} and \code{A} are both averaged in this way.

If \code{x} is of mode \code{"character"}, then the duplicate values are assumed to be equal and the first is taken as the average.
\end{Details}
\begin{Value}
A data object of the same class as \code{x} with \code{1/ndups} as many rows.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{dimnames}{dimnames}} in the base package.

\LinkA{02.Classes}{02.Classes} gives an overview of data classes used in LIMMA.
\end{SeeAlso}

