GSE84105 Processing Pipeline

Publication

Immunity (2020) — PMID 32433949

Dataset

Defining memory-like CD8 T cells that respond to PD-1 therapy in chronic viral infection

1. 1

   Data was normalized using RMAExpress.

   RMAExpress vNot specified (Inferred with models/gemini-2.5-flash)

   $ Bash example

   # The original RMAExpress is a GUI application. This code block demonstrates how to perform Robust Multi-array Average (RMA) normalization using the 'affy' Bioconductor package in R, which implements the same algorithm.
   
   # Install R and Bioconductor if not already present
   # R
   # if (!requireNamespace("BiocManager", quietly = TRUE))
   #     install.packages("BiocManager")
   # BiocManager::install("affy")
   
   # Create an R script for RMA normalization
   cat << 'EOF' > normalize_rma.R
   library(affy)
   
   # Get CEL file paths from command line arguments
   # The first argument is expected to be the directory containing CEL files.
   args <- commandArgs(trailingOnly = TRUE)
   if (length(args) == 0) {
     stop("Please provide the path to the directory containing CEL files as the first argument.", call. = FALSE)
   }
   cel_dir <- args[1]
   output_file <- "rma_normalized_data.txt"
   
   # List all .CEL files in the specified directory
   cel_files <- list.files(path = cel_dir, pattern = "\\.CEL$", full.names = TRUE)
   if (length(cel_files) == 0) {
     stop(paste("No .CEL files found in directory:", cel_dir), call. = FALSE)
   }
   
   message(paste("Found", length(cel_files), "CEL files in", cel_dir))
   message("Reading CEL files...")
   data <- ReadAffy(filenames = cel_files)
   
   message("Performing RMA normalization...")
   eset <- rma(data)
   
   # Extract normalized expression matrix
   normalized_matrix <- exprs(eset)
   
   # Write normalized data to a tab-separated file
   write.table(normalized_matrix, file = output_file, sep = "\t", quote = FALSE, row.names = TRUE)
   
   message(paste("RMA normalized data written to", output_file))
   EOF
   
   # Execute the R script
   # Replace 'path/to/your/cel_files_directory' with the actual directory containing your .CEL files
   Rscript normalize_rma.R path/to/your/cel_files_directory

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