--- a
+++ b/R/preprocessCELFiles.R
@@ -0,0 +1,85 @@
+#' RMA preprocess CEL files
+#'
+#' General function for RMA processing microarray data. Automatically downloads
+#' custom Brainarray chip definition files (cdf) if wanted.
+#'
+#' @param cel_files A character vector of .CEL files.
+#' @param cdf A character specifying the CDF type to use. Should be either
+#'   \code{"brainarray"} or \code{"affy"}.
+#' @param 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.
+#' @param version A character giving the brainarray version to be used.
+#'   Only used if \code{cdf} is \code{"brainarray"}. See \code{listVersions()}.
+#' @param background boolean. Should RMA background correction be performed?
+#' @param normalize boolean. Should RMA normalization be performed?
+#' @return An expression set object.
+#' @importFrom affy read.affybatch just.rma
+#' @importFrom affyio read.celfile.header
+#' @importFrom oligo rma
+#' @export
+preprocessCELFiles <- function(cel_files,
+                               cdf = c("affy", "brainarray"),
+                               target,
+                               version = getLatestVersion(),
+                               background = TRUE,
+                               normalize = TRUE) {
+  getCDF <- function(file) {
+    return(read.celfile.header(file)$cdfName)
+  }
+  array_type <- sapply(cel_files, getCDF)
+  array_types <- unique(array_type)
+  if (length(array_types) != 1) {
+    stop("The CEL files are from more that one array platform. The unique ",
+         "platforms are: ", paste(array_types, collapse = ", "),
+         ". The arrays should be preprocessed in batches of array platforms.")
+  }
+  array_type <- array_type[1]
+  cel_files <- normalizePath(cel_files)
+  cdf <- match.arg(cdf)
+
+  if (tolower(cdf) == "affy") {
+    # Load expression set
+    es <- oligo::read.celfiles(cel_files)
+
+    # RMA normalize
+    if (class(es) %in% c("ExonFeatureSet","HTAFeatureSet","GeneFeatureSet")) {
+      if (missing(target)) stop("No target provided.")
+      es_rma <- oligo::rma(es, background = background,
+                           normalize = normalize, target = target)
+      attr(es_rma, "target") <- target
+    } else {
+      es_rma <- oligo::rma(es, background = background,
+                           normalize = normalize)
+      attr(es_rma, "target") <- NULL
+    }
+
+  } else if (tolower(cdf) == "brainarray") {
+
+    if (missing(target)) stop("No target provided.")
+
+    req <- requireBrainarray(array_type = array_type,
+                             custom_cdf = target,
+                             version = version)
+    suppressWarnings({
+      es_rma <- just.rma(filenames = cel_files,
+                         verbose = TRUE,
+                         cdfname = getCustomCDFName(req$brain_dat, array_type))
+    })
+    attr(es_rma, "target") <- target
+
+  } else {
+    stop("cdf == '", cdf,
+         "' not supported. Should be either 'affy' or 'brainarray'")
+  }
+
+  # Add attributes
+  attr(es_rma, "cdf") <- cdf
+  attr(es_rma, "version") <- version
+  attr(es_rma, "background") <- background
+  attr(es_rma, "normalize") <- normalize
+
+  return(es_rma)
+}