% Generated by roxygen2 (4.1.1): do not edit by hand

% Please edit documentation in R/preprocessCELFiles.R

\name{preprocessCELFiles}

\alias{preprocessCELFiles}

\title{RMA preprocess CEL files}

\usage{

preprocessCELFiles(cel_files, cdf = c("affy", "brainarray"), target,

  version = getLatestVersion(), background = TRUE, normalize = TRUE)

}

\arguments{

\item{cel_files}{A character vector of .CEL files.}

\item{cdf}{A character specifying the CDF type to use. Should be either

\code{"brainarray"} or \code{"affy"}.}

\item{target}{Specifies the "target" CDF to use depending on \code{cdf}.

If \code{cdf} is \code{"affy"} then \code{target} is e.g. \code{"core"}.

If \code{cdf} is \code{"brainarray"} then \code{target} is

e.g. \code{"ensg"}, \code{"entrez"}.

See \code{listTargets()} to list the available targets.}

\item{version}{A character giving the brainarray version to be used.

Only used if \code{cdf} is \code{"brainarray"}. See \code{listVersions()}.}

\item{background}{boolean. Should RMA background correction be performed?}

\item{normalize}{boolean. Should RMA normalization be performed?}

}

\value{

An expression set object.

}

\description{

General function for RMA processing microarray data. Automatically downloads

custom Brainarray chip definition files (cdf) if wanted.

}