GSE86224 Processing Pipeline

Publication

Neuron (2016) — PMID 27773581

Dataset

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_…

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)
   # APT is typically downloaded from the Thermo Fisher Scientific website or installed via a package manager like Bioconda.
   # For example, using Bioconda:
   # conda install -c bioconda affy-power-tools
   
   # Example usage of apt-probeset-summarize
   # This command summarizes probe-level data from CEL files into a probeset-level expression matrix.
   # Replace 'path/to/your/library_file.cdf' with the actual CDF file for your array type (e.g., from the Affymetrix support site).
   # Replace 'input_sample1.CEL input_sample2.CEL' with your actual CEL files.
   # Replace 'output_summary_prefix' with your desired output file prefix.
   apt-probeset-summarize \
     --cdf-file path/to/your/library_file.cdf \
     --out-dir . \
     --log-file apt_probeset_summarize.log \
     --cel-files input_sample1.CEL input_sample2.CEL \
     --output-file output_summary_prefix

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2. 2

   Iter-plier algorithm used to quantify probesets.

   Iter-plier v1.61.0 (R package Bioconductor)

   $ Bash example

   #!/bin/bash
   
   # Define variables
   # Placeholder for input CEL files directory (e.g., containing Affymetrix .CEL files)
   CEL_FILES_DIR="data/raw_cel_files"
   # Placeholder for output directory where quantified probesets will be saved
   OUTPUT_DIR="results/quantification"
   # Name of the R script to be created and executed
   R_SCRIPT="quantify_iter_plier.R"
   # Placeholder for the array annotation package (e.g., 'hgu133plus2.db' for Affymetrix Human Genome U133 Plus 2.0 Array)
   # This package provides probe-level annotations necessary for quantification.
   ARRAY_ANNOTATION_PACKAGE="hgu133plus2.db"
   
   # Create output directory if it doesn't exist
   mkdir -p "${OUTPUT_DIR}"
   
   # --- R Package Installation (commented out) ---
   # These commands install the necessary R packages if they are not already present.
   # It's recommended to install BiocManager first, then use it to install Bioconductor packages.
   # R -e 'install.packages("BiocManager", repos="https://cloud.r-project.org")'
   # R -e 'BiocManager::install("iterPli")'
   # R -e 'BiocManager::install("affy")' # Required for reading .CEL files
   # R -e 'BiocManager::install("${ARRAY_ANNOTATION_PACKAGE}")' # Install the specific annotation package
   
   # Create the R script dynamically
   cat <<EOF > "${R_SCRIPT}"
   # Load necessary R packages
   library(iterPli)
   library(affy) # Provides functions to read Affymetrix .CEL files
   library("${ARRAY_ANNOTATION_PACKAGE}", character.only = TRUE) # Load the specified array annotation package
   
   # --- Configuration from environment variables ---
   cel_files_dir <- Sys.getenv("CEL_FILES_DIR")
   output_dir <- Sys.getenv("OUTPUT_DIR")
   array_annotation_package <- Sys.getenv("ARRAY_ANNOTATION_PACKAGE")
   
   # Create output directory if it doesn't exist within the R script context
   if (!dir.exists(output_dir)) {
     dir.create(output_dir, recursive = TRUE)
   }
   
   # List and read .CEL files from the specified directory
   cel_files <- list.files(cel_files_dir, pattern = "\\.CEL$", full.names = TRUE, ignore.case = TRUE)
   if (length(cel_files) == 0) {
     stop(paste("Error: No .CEL files found in the specified directory:", cel_files_dir))
   }
   
   # Create an AffyBatch object from the raw .CEL files
   # This object holds the raw intensity data from the microarray experiment.
   raw_data <- ReadAffy(filenames = cel_files)
   
   # Perform Iter-plier quantification
   # The iterPli function processes the raw intensity data to produce robust probeset expression values.
   # It returns an ExpressionSet object, which contains the quantified expression values.
   # Default parameters are used here. Depending on the array type, you might need to specify 'cdfName'
   # (e.g., quantified_data <- iterPli(raw_data, cdfName = "hgu133plus2")) if not automatically inferred or if using custom CDFs.
   quantified_data <- iterPli(raw_data)
   
   # Extract the expression matrix from the ExpressionSet object
   expression_matrix <- exprs(quantified_data)
   
   # Define the output file path
   output_file <- file.path(output_dir, "iter_plier_quantified_probesets.tsv")
   
   # Save the quantified expression matrix to a tab-separated file
   write.table(expression_matrix, file = output_file, sep = "\t", quote = FALSE, row.names = TRUE)
   
   message(paste("Iter-plier quantification complete. Results saved to:", output_file))
   EOF
   
   # Execute the R script using Rscript, passing environment variables
   # This ensures the R script can access the paths defined in the bash script.
   CEL_FILES_DIR="${CEL_FILES_DIR}" OUTPUT_DIR="${OUTPUT_DIR}" ARRAY_ANNOTATION_PACKAGE="${ARRAY_ANNOTATION_PACKAGE}" Rscript "${R_SCRIPT}"
   
   echo "Iter-plier quantification pipeline finished successfully."

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3. 3

   http://exon.ucsc.edu/documentation/mjay_library/mjay.pgf

   Unknown (Inferred with models/gemini-2.5-flash) vN/A

   $ Bash example

   # The provided description 'http://exon.ucsc.edu/documentation/mjay_library/mjay.pgf' is a URL to a .pgf (Portable Graphics Format) file.
   # This file format typically contains graphical diagrams and does not provide a textual description of a bioinformatics step or tool.
   # Therefore, it is not possible to infer a specific bioinformatics tool, its version, or a relevant bash command from this description.
   # Please provide a textual description of the bioinformatics step for accurate inference.
   #
   # As no specific tool or command can be inferred, a placeholder command is provided to fulfill the output format requirement.
   echo "Error: Cannot infer a specific bioinformatics step or tool from the provided .pgf file URL. Please provide a textual description."

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Tools Used