GSE33113 Processing Pipeline

Publication

Life science alliance (2020) — PMID 32817263

Dataset

AMC colon cancer AJCCII

1. 1

   Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

   Microarray vMAS5.0 GitHub

   $ Bash example

   # The original normalization was performed using proprietary Affymetrix GCOS software.
   # This code block demonstrates the equivalent MAS5.0 normalization using the open-source Bioconductor 'affy' package in R.
   
   # Install R and Bioconductor if not already present
   # sudo apt-get update && sudo apt-get install -y r-base
   # R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("affy")'
   
   # Define input and output paths
   INPUT_CEL_DIR="path/to/your/cel_files"
   OUTPUT_DIR="path/to/output_normalized_data"
   mkdir -p "${OUTPUT_DIR}"
   
   # R script for MAS5.0 normalization
   Rscript -e '
     library(affy)
     
     # Set input and output directories
     input_cel_dir <- Sys.getenv("INPUT_CEL_DIR")
     output_dir <- Sys.getenv("OUTPUT_DIR")
     
     # Read CEL files
     cel_files <- list.files(input_cel_dir, pattern = "\\.cel$", full.names = TRUE, ignore.case = TRUE)
     if (length(cel_files) == 0) {
       stop("No CEL files found in the specified directory.")
     }
     
     # Create an AffyBatch object
     raw_data <- ReadAffy(filenames = cel_files)
     
     # Perform MAS5.0 normalization with target signal = 100
     # The "target" parameter in mas5() corresponds to the target signal value.
     normalized_data <- mas5(raw_data, target = 100)
     
     # Extract expression matrix
     expr_matrix <- exprs(normalized_data)
     
     # Save the normalized expression matrix to a CSV file
     output_file <- file.path(output_dir, "normalized_mas5_expression.csv")
     write.csv(expr_matrix, file = output_file, row.names = TRUE)
     
     message(paste("MAS5.0 normalized expression data saved to:", output_file))
   '
   

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