#' @rdname cleanMetadata

#' @details

#'    GSE56315:\cr

#'    The cleanup of GSE56315 (CHEPRETRO) adds two batches corresponding to each

#'    clinical samples and normal sorted tissues both on platform

#'    HG-U133 plus 2.

#' @export

cleanMetadata.GSE56315 <- function(meta_data) {

  message("Cleaning GSE56315 (CHEPRETRO)!")

  # Generic clean

  suppressMessages(meta_data <- cleanMetadata.data.frame(meta_data))

  # Added factor describing the batches and CEL files

  tmp <- as.character(meta_data$characteristics_ch1)

  tmp <- ifelse(tmp == "tissue: human healthy tonsils", "tonsil", "DLBCL")

  meta_data$Batch <- factor(tmp)

  meta_data$CEL <-

    gsub("^.+/(GSM[0-9]+)\\..+$", "\\1", meta_data$supplementary_file)

  meta_data$GSM <- as.character(meta_data$geo_accession)

  # rownames(meta_data) <- meta_data$CEL

  return(meta_data)

}