GSE40653 Processing Pipeline

Publication

Nature neuroscience (2012) — PMID 23023293

Dataset

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

1. 1

   Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize.

   Microarray vInferred with models/gemini-2.5-flash

   $ Bash example

   # Install Affymetrix Power Tools (APT)
   # conda install -c bioconda affymetrix-power-tools
   
   # Define input and output paths
   # Replace with actual CEL files and the correct CDF file for your array type
   CEL_FILES="sample1.CEL sample2.CEL sample3.CEL" # Placeholder for actual CEL files
   CDF_FILE="HG-U133A.cdf" # Placeholder for the specific array's CDF file (e.g., from Affymetrix support site)
   OUTPUT_DIR="apt_summarize_output"
   ALGORITHM="rma" # Common summarization algorithm (e.g., rma, mas5, dabg)
   
   # Create output directory if it doesn't exist
   mkdir -p "${OUTPUT_DIR}"
   
   # Execute apt-probeset-summarize
   apt-probeset-summarize \
       -a "${ALGORITHM}" \
       -o "${OUTPUT_DIR}" \
       -c "${CDF_FILE}" \
       ${CEL_FILES}

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2. 2

   Iter-plier algorithm used to quantify probesets.

   plier (R package) (Inferred with models/gemini-2.5-flash) v(Inferred with models/gemini-2.5-flash) 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(c('plier', 'affy'))"
   
   cat << 'EOF' > run_plier.R
   # Load necessary R packages
   library(plier)
   library(affy) # Required for ReadAffy
   
   # Define input CEL files directory and output file
   # IMPORTANT: Replace "path/to/your/raw_cel_files" with the actual directory containing your .CEL files.
   cel_files_dir <- Sys.getenv("CEL_FILES_DIR", "path/to/your/raw_cel_files")
   output_file <- Sys.getenv("OUTPUT_FILE", "probeset_quantification_plier.tsv")
   
   # Check if the CEL files directory exists
   if (!dir.exists(cel_files_dir)) {
     stop(paste("Error: CEL files directory not found:", cel_files_dir,
                "\nPlease update the 'CEL_FILES_DIR' environment variable to point to your actual .CEL files."))
   }
   
   # Read CEL files into an AffyBatch object
   # This step requires valid Affymetrix .CEL files.
   # Ensure that the appropriate annotation package for your array type is installed
   # if you plan to use it for downstream analysis (e.g., hgu133plus2.db).
   # Example: BiocManager::install("hgu133plus2.db")
   raw_data <- ReadAffy(celfile.path = cel_files_dir)
   
   # Perform PLIER quantification
   # The 'plier' function implements the Iter-plier algorithm.
   eset_plier <- plier(raw_data)
   
   # Extract expression values (log2 transformed)
   expression_matrix <- exprs(eset_plier)
   
   # Write results to a TSV file
   write.table(expression_matrix, file = output_file, sep = "\t", quote = FALSE, row.names = TRUE)
   
   message(paste("PLIER quantification complete. Results saved to:", output_file))
   EOF
   
   # Set environment variables for the R script
   # IMPORTANT: Replace "path/to/your/raw_cel_files" with the actual directory containing your .CEL files
   export CEL_FILES_DIR="path/to/your/raw_cel_files"
   export OUTPUT_FILE="probeset_quantification_plier.tsv"
   
   # Execute the R script
   Rscript run_plier.R

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Tools Used