GSE35008 Processing Pipeline

Publication

Nature communications (2022) — PMID 35781533

Dataset

Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with normal karyotype and healthy…

1. 1

   Data were normalized normalized with the Expression Console Software version 1.1 from Affymetrix using Robust Multi-array Average (RMA) algorithm.

   Microarray v1.1

   $ Bash example

   # Expression Console Software is a GUI-based application. It is not typically run via command-line.
   #
   # Manual steps within Expression Console Software (version 1.1):
   # 1. Launch Expression Console Software.
   # 2. Load Affymetrix .CEL files (raw data) for the experiment.
   # 3. Select the loaded files for analysis.
   # 4. Choose "Analysis" -> "GeneChip Analysis" or similar option.
   # 5. In the analysis settings, select "Robust Multi-array Average (RMA)" as the normalization algorithm.
   # 6. Specify output directory and file format (e.g., tab-delimited text file for expression matrix).
   # 7. Run the analysis to generate normalized expression values.
   #
   # Input: Affymetrix .CEL files
   # Output: Normalized expression matrix (e.g., .txt, .csv)

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2. 2

   MEV software was used to select differentially expressed genes by applying the following criteria: (a) Absolute value of the group mean difference greater than 1.5, and (b) p value smaller than 0.05 (Welch's t test)

   MEV v(Inferred with models/gemini-2.5-flash) GitHub

   $ Bash example

   # MEV (MultiExperiment Viewer) is primarily a graphical user interface (GUI) software
   # for microarray and RNA-seq data analysis. The described differential expression
   # analysis and filtering steps are typically performed interactively within the MEV GUI.
   #
   # The following command is a conceptual representation of how these parameters and
   # methods would be applied if MEV had a direct command-line interface for this task.
   # In practice, these steps are executed through menu selections and dialog boxes in the MEV GUI.
   
   # Placeholder for input data:
   # EXPRESSION_MATRIX="your_expression_data.txt" # e.g., tab-delimited gene expression matrix
   # GROUP_INFO="your_group_definitions.txt"     # e.g., file mapping samples to groups
   # OUTPUT_FILE="differentially_expressed_genes.txt"
   
   mev_cli --input "${EXPRESSION_MATRIX}" \
           --groups "${GROUP_INFO}" \
           --test welch_t_test \
           --min-abs-mean-diff 1.5 \
           --max-pvalue 0.05 \
           --output "${OUTPUT_FILE}"

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Tools Used