\HeaderA{modifyWeights}{modifyWeights}{modifyWeights}
\keyword{hplot}{modifyWeights}
\begin{Description}\relax
Modify weights matrix for given gene status values.
\end{Description}
\begin{Usage}
\begin{verbatim}
modifyWeights(weights=rep(1,length(status)), status, values, multipliers)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{weights}] numeric matrix of relative weights, rows corresponding to genes and columns to arrays
\item[\code{status}] character vector giving the control status of each spot on the array, of same length as the number of rows of \code{weights}
\item[\code{values}] character vector giving subset of the unique values of \code{status}
\item[\code{multipliers}] numeric vector of same length as \code{values} giving factor by which weights will be modified
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function is usually used to temporarily modify the weights matrix during normalization of data.
The function can be used for example to give zero weight to spike-in ratio control spots during normalization.
\end{Details}
\begin{Value}
Numeric matrix of same dimensions as \code{weights} with rows corresponding to \code{values} in \code{status} modified by the specified multipliers.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of normalization functions available in LIMMA is given in \LinkA{05.Normalization}{05.Normalization}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
w <- matrix(runif(6*3),6,3)
status <- c("Gene","Gene","Ratio_Control","Ratio_Control","Gene","Gene")
modifyWeights(w,status,values="Ratio_Control",multipliers=0)
\end{ExampleCode}
\end{Examples}

