GSE54964 Processing Pipeline

Publication

Circulation (2015) — PMID 25739401

Dataset

Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Affymetrix]

1. 1

   CEL files were analyzed using the oligo package in R/Bioconductor and normalized using RMA

   R vInferred from description GitHub

   $ Bash example

   # Install R and Bioconductor (if not already installed)
   # sudo apt-get update
   # sudo apt-get install r-base
   # R -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager'); BiocManager::install('oligo')"
   
   # Create an R script for oligo processing and RMA normalization
   cat << 'EOF' > process_cel_files.R
   library(oligo)
   
   # Define the directory containing CEL files
   # Replace '.' with the actual path to your CEL files if they are not in the current directory
   cel_files_dir <- "."
   
   # List all CEL files in the specified directory
   cel_files <- list.celfiles(path = cel_files_dir, full.names = TRUE, pattern = "\\.CEL$|\\.cel$")
   
   if (length(cel_files) == 0) {
       stop("No CEL files found in the specified directory: ", cel_files_dir)
   }
   
   message("Found CEL files: ", paste(basename(cel_files), collapse = ", "))
   
   # Read CEL files into an appropriate oligo object (e.g., GeneFeatureSet, ExpressionFeatureSet)
   raw_data <- read.celfiles(cel_files)
   
   message("Performing RMA normalization...")
   # Perform RMA normalization
   normalized_data <- rma(raw_data)
   
   # Extract normalized expression matrix
   exprs_matrix <- exprs(normalized_data)
   
   # Define output file name
   output_file <- "normalized_expression_rma.tsv"
   
   # Save normalized expression matrix to a tab-separated file
   write.table(exprs_matrix, file = output_file, sep = "\t", quote = FALSE, row.names = TRUE)
   
   message("RMA normalization complete. Normalized expression saved to: ", output_file)
   EOF
   
   # Execute the R script
   Rscript process_cel_files.R

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