GSE74250 Processing Pipeline

Publication

Nature structural & molecular biology (2016) — PMID 27775709

Dataset

Transcriptome analysis of diverse cell types infected with human cytomegalovirus

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) - specific installation steps vary by OS and version.
   # Please refer to the official Thermo Fisher Scientific documentation for the most up-to-date installation instructions.
   # Example for Linux (check official documentation for latest instructions):
   # wget https://assets.thermofisher.com/TFS-Assets/LSG/software/APT_2.11.2_Linux.zip
   # unzip APT_2.11.2_Linux.zip
   # cd APT_2.11.2_Linux
   # ./install.sh
   
   # Ensure APT executables are in your PATH
   # export PATH="/path/to/APT/bin:$PATH"
   
   # Placeholder for input CEL files. Create a file named 'input_celfiles.txt'
   # containing the paths to your .CEL files, one path per line.
   # Example: 
   # echo "/path/to/sample1.CEL" > input_celfiles.txt
   # echo "/path/to/sample2.CEL" >> input_celfiles.txt
   
   # Placeholder for a CDF (Chip Description File) or PGF (Probe Group File).
   # You must download the appropriate CDF/PGF file for your specific Affymetrix array type
   # from the Thermo Fisher Scientific website. For example, 'human_hg19.cdf' is a placeholder
   # for a human array based on the hg19 genome assembly.
   # Example download (replace with actual file for your array):
   # wget https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/HuGene-1_0-st-v1.cdf -O human_hg19.cdf
   
   # Create an output directory for the summarized data
   mkdir -p apt_summarize_output
   
   # Run apt-probeset-summarize using the RMA (Robust Multi-array Average) algorithm.
   # -a rma: Specifies the RMA algorithm for background correction, normalization, and summarization.
   # --cel-files: Specifies a file containing a list of CEL file paths, one per line.
   # --cdf-file: Specifies the CDF or PGF file corresponding to the array type used.
   # -o apt_summarize_output: Specifies the output directory where summarized data will be stored.
   apt-probeset-summarize -a rma \
     --cel-files input_celfiles.txt \
     --cdf-file human_hg19.cdf \
     -o apt_summarize_output

   Copy
2. 2

   Iter-plier algorithm used to quantify probesets.

   iterpliertool (Inferred with models/gemini-2.5-flash) vAPT 1.18.0 (Inferred with models/gemini-2.5-flash)

   $ Bash example

   # Install Affymetrix Power Tools (APT)
   # conda install -c bioconda affymetrix-power-tools
   
   # Define input CEL files (replace with actual file paths)
   CEL_FILES="sample1.CEL sample2.CEL sample3.CEL"
   
   # Define the Chip Description File (CDF) for the specific array type (replace with actual CDF path)
   # Example for a common array: HG-U133_Plus_2.cdf
   CDF_FILE="path/to/your/array_type.cdf"
   
   # Define the output file name for the probeset quantification
   OUTPUT_FILE="probeset_quantification.txt"
   
   # Execute iterpliertool to quantify probesets using the Iter-PLIER algorithm
   # The --cel-files argument can take multiple CEL files separated by spaces
   # The --cdf-file argument specifies the CDF file for probe set definitions
   # The --output-file argument specifies the output file for the summarization results
   iterpliertool --cel-files "${CEL_FILES}" --cdf-file "${CDF_FILE}" --output-file "${OUTPUT_FILE}"

   Copy
3. 3

   As previously described (Huelga et al., 2012).

   Not specified (Inferred with models/gemini-2.5-flash) vNot specified

   $ Bash example

   # No specific command or parameters can be inferred from 'As previously described (Huelga et al., 2012)'.
   # This description refers to a methodology detailed in the cited publication, not a specific software tool or command.

   Copy
4. 4

   HJAY_r2.pgf

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

   $ Bash example

   # This command is a placeholder for the custom script "HJAY_r2.pgf".
   # The specific tool, version, and parameters are not provided in the description.
   # Replace 'input.bam', 'output.tsv', and 'hg38' with actual file paths and reference genome.
   # Reference genome 'hg38' is used as a common placeholder for the latest human assembly.
   
   # Example execution of a custom script.
   # Assuming HJAY_r2.pgf is an executable script or needs an interpreter like bash/python.
   # For demonstration, we'll assume it's a bash script.
   bash HJAY_r2.pgf \
       --input_file "input.bam" \
       --output_file "output.tsv" \
       --genome_assembly "hg38"

   Copy

Tools Used