GSE35338 Processing Pipeline

Publication

Genome medicine (2016) — PMID 27655340

Dataset

Expression data from reactive astrocytes acutely purified from young adult mouse brains

1. 1

   CEL files were analyzed wth the Arraystar 4.0 software (DNAstar) using RMA processing with quantile normalization.

   Arraystar v4.0

   $ Bash example

   # Arraystar 4.0 is a commercial, GUI-based software. The following R code provides a conceptual command-line equivalent for RMA processing with quantile normalization, commonly performed on CEL files, using the 'affy' package. This is a programmatic approximation of the described analysis step.
   
   # Install R if not already installed (e.g., on Ubuntu/Debian)
   # sudo apt-get update
   # sudo apt-get install r-base
   
   # Install Bioconductor and 'affy' package in R
   # R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("affy")'
   
   # Create an R script to perform RMA and quantile normalization
   cat << 'EOF' > analyze_cel_files.R
   library(affy)
   
   # Define the directory containing CEL files
   cel_dir <- "." # Assuming CEL files are in the current directory
   # Or specify a path: cel_dir <- "/path/to/your/cel_files"
   
   # List all CEL files
   cel_files <- list.files(path = cel_dir, pattern = "\\.CEL$", full.names = TRUE, ignore.case = TRUE)
   
   if (length(cel_files) == 0) {
     stop("No CEL files found in the specified directory.")
   }
   
   # Read CEL files
   print(paste("Reading", length(cel_files), "CEL files..."))
   affy_batch <- ReadAffy(filenames = cel_files)
   
   # Perform RMA processing with quantile normalization
   print("Performing RMA processing with quantile normalization...")
   eset <- rma(affy_batch)
   
   # Extract expression matrix
   expression_matrix <- exprs(eset)
   
   # Save the normalized expression matrix to a CSV file
   output_file <- "normalized_expression_matrix.csv"
   write.csv(expression_matrix, file = output_file)
   
   print(paste("Analysis complete. Normalized expression matrix saved to", output_file))
   EOF
   
   # Execute the R script
   Rscript analyze_cel_files.R

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