Added GC-RMA support for Affymetrix arrays.

DESCRIPTION

@@ -14,6 +14,7 @@ Imports:
     utils,
     stats,
     affy,
+    gcrma,
     arrayQualityMetrics,
     SCAN.UPC,
     massiR,

R/preprocess_data.R

@@ -47,14 +47,14 @@ preprocess_data <- function(input_data_dir, output_data_file,
                                               batch_filename   = batch_filename,
                                               clean_samples    = clean_samples,
                                               verbose          = verbose)
-    } else if (method == "RMA") {
-      eset <- preprocess_data_affymetrix_rma(input_data_dir,
-                                             output_data_file,
-                                             compressed       = compressed,
-                                             batch_correction = batch_correction,
-                                             batch_filename   = batch_filename,
-                                             clean_samples    = clean_samples,
-                                             verbose          = verbose)
+    } else if (method == "GCRMA") {
+      eset <- preprocess_data_affymetrix_gcrma(input_data_dir,
+                                               output_data_file,
+                                               compressed       = compressed,
+                                               batch_correction = batch_correction,
+                                               batch_filename   = batch_filename,
+                                               clean_samples    = clean_samples,
+                                               verbose          = verbose)
     }
   } else if (platform == "Agilent") {
     eset <- preprocess_data_agilent_limma(input_data_dir,

R/preprocess_data_affymetrix_rma.R → R/preprocess_data_affymetrix_gcrma.R

-#' @title Preprocess an Affymetrix dataset with RMA.
+#' @title Preprocess an Affymetrix dataset with GC-RMA.
 #'
 #' @description This function preprocess an Affymetrix dataset using RMA and saves the
 #' results in a given TSV file. In addition, it returns the ESET object.
@@ -22,7 +22,7 @@
 #' @param verbose A boolean representing whether the function should display log information. This
 #'  is TRUE by default.
 #' @return The expression data as an ESET object.
-preprocess_data_affymetrix_rma <- function(input_data_dir, output_data_file,
+preprocess_data_affymetrix_gcrma <- function(input_data_dir, output_data_file,
                                            compressed       = FALSE,
                                            batch_correction = FALSE,
                                            batch_filename   = "Batch.tsv",
@@ -36,7 +36,7 @@ preprocess_data_affymetrix_rma <- function(input_data_dir, output_data_file,
   input_data_files <- affy::list.celfiles(raw_data_input_dir, full.names = TRUE)
   remove(raw_data_input_dir)
   batch <- affy::ReadAffy(filenames = input_data_files, compress = compressed, verbose = verbose)
-  eset <- affy::rma(batch)
+  eset  <- gcrma::gcrma(batch)
 
   # If necessary, we remove the samples that do not have clinical data.
   if (clean_samples) {