--- a +++ b/R/cleanMetadata.GSE11318.R @@ -0,0 +1,22 @@ +#' @rdname cleanMetadata +#' @details +#' GSE11318:\cr +#' The cleanup of GSE11318 (NCI) adds the batch corresponding to +#' platform GPL570 (HG-U133 plus 2) and excludes the GPL6400 samples. +#' @export +cleanMetadata.GSE11318 <- function(meta_data) { + message("Cleaning GSE34171 (NCI)!") + + # Generic clean + suppressMessages(meta_data <- cleanMetadata.data.frame(meta_data)) + + # Added factor describing the batches and CEL files + meta_data$Batch <- factor(meta_data$platform_id, + levels = c("GPL570", NA)) + 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) +}