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\name{rma.background.correct}
\alias{rma.background.correct}
\title{RMA Background Correction}
\description{Background correct each column of a matrix
}
\usage{
rma.background.correct(x,copy=TRUE)
}
\arguments{
\item{x}{A matrix of intensities where each column corresponds to a
chip and each row is a probe.}
\item{copy}{Make a copy of matrix before background correctiong. Usually safer to
work with a copy, but in certain situations not making a copy of the
matrix, but instead background correcting it in place will be more memory friendly.}
}
\details{
Assumes PMs are a convolution of normal and exponentional. So we
observe X+Y where X is backround and Y is signal. \code{bg.adjust}
returns E[Y|X+Y, Y>0] as our backround corrected
PM.
}
\value{
A RMA background corrected \code{matrix}.
}
\references{
Bolstad, BM (2004) \emph{Low Level Analysis of High-density
Oligonucleotide Array Data: Background, Normalization and
Summarization}. PhD Dissertation. University of California,
Berkeley. pp 17-21
}
\author{Ben Bolstad, \email{bmbolstad.com}}
\keyword{manip}
|
