Commit 7cb20fd2 authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Added GC-RMA support for Affymetrix arrays.

parent fdeae68b
...@@ -14,6 +14,7 @@ Imports: ...@@ -14,6 +14,7 @@ Imports:
utils, utils,
stats, stats,
affy, affy,
gcrma,
arrayQualityMetrics, arrayQualityMetrics,
SCAN.UPC, SCAN.UPC,
massiR, massiR,
......
...@@ -47,14 +47,14 @@ preprocess_data <- function(input_data_dir, output_data_file, ...@@ -47,14 +47,14 @@ preprocess_data <- function(input_data_dir, output_data_file,
batch_filename = batch_filename, batch_filename = batch_filename,
clean_samples = clean_samples, clean_samples = clean_samples,
verbose = verbose) verbose = verbose)
} else if (method == "RMA") { } else if (method == "GCRMA") {
eset <- preprocess_data_affymetrix_rma(input_data_dir, eset <- preprocess_data_affymetrix_gcrma(input_data_dir,
output_data_file, output_data_file,
compressed = compressed, compressed = compressed,
batch_correction = batch_correction, batch_correction = batch_correction,
batch_filename = batch_filename, batch_filename = batch_filename,
clean_samples = clean_samples, clean_samples = clean_samples,
verbose = verbose) verbose = verbose)
} }
} else if (platform == "Agilent") { } else if (platform == "Agilent") {
eset <- preprocess_data_agilent_limma(input_data_dir, eset <- preprocess_data_agilent_limma(input_data_dir,
......
#' @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 #' @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. #' results in a given TSV file. In addition, it returns the ESET object.
...@@ -22,7 +22,7 @@ ...@@ -22,7 +22,7 @@
#' @param verbose A boolean representing whether the function should display log information. This #' @param verbose A boolean representing whether the function should display log information. This
#' is TRUE by default. #' is TRUE by default.
#' @return The expression data as an ESET object. #' @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, compressed = FALSE,
batch_correction = FALSE, batch_correction = FALSE,
batch_filename = "Batch.tsv", batch_filename = "Batch.tsv",
...@@ -36,7 +36,7 @@ preprocess_data_affymetrix_rma <- function(input_data_dir, output_data_file, ...@@ -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) input_data_files <- affy::list.celfiles(raw_data_input_dir, full.names = TRUE)
remove(raw_data_input_dir) remove(raw_data_input_dir)
batch <- affy::ReadAffy(filenames = input_data_files, compress = compressed, verbose = verbose) 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 necessary, we remove the samples that do not have clinical data.
if (clean_samples) { if (clean_samples) {
......
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